genome.fa.s25.2.7.7.80.10.50.1000.10.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  10  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)
1920491--1920540	16	3.2	15	72	27	50	44	0	0	56	0.99
1920482--1920562	32	2.4	34	84	12	105	44	1	0	54	1.08
1920465--1920553	31	3.2	26	74	20	72	43	0	0	56	0.99
1923522--1923549	3	9.3	3	100	0	56	64	0	0	35	0.94
1933073--1933154	41	2.0	41	95	0	146	35	8	15	40	1.78
1937342--1937375	2	17.0	2	93	0	59	2	47	0	50	1.16
1941733--1941757	2	12.5	2	100	0	50	48	0	0	52	1.00
1947275--1947311	17	2.2	17	90	0	56	32	43	2	21	1.67
1948131--1948170	3	13.3	3	89	0	62	65	0	32	2	1.06
1951760--1951788	2	14.5	2	100	0	58	0	48	0	51	1.00
1952960--1953024	32	2.0	32	100	0	130	27	15	6	50	1.67
1952968--1953019	16	3.2	16	70	20	54	28	13	5	51	1.64
1955050--1955118	25	2.7	26	80	17	74	55	0	0	44	0.99
1963771--1963826	24	2.3	24	96	0	103	35	26	23	14	1.93
1975073--1975097	2	12.5	2	100	0	50	0	48	0	52	1.00
1975568--1975600	16	2.1	16	94	0	57	51	15	0	33	1.43
1975562--1975604	20	2.2	20	95	0	77	51	18	0	30	1.47
1975566--1975602	18	2.1	18	100	0	74	51	16	0	32	1.45
1981060--1981123	22	2.9	22	82	17	71	50	1	1	46	1.20
1983368--1983443	16	4.6	16	71	14	64	65	1	0	32	1.01
1983385--1983435	7	7.4	7	76	12	52	66	1	0	31	1.03
1983385--1983450	35	1.9	35	87	9	100	66	1	0	31	1.01
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1983384--1983438	20	2.7	19	78	10	65	67	1	0	30	1.01
1983385--1983453	20	3.5	19	77	16	61	65	1	0	33	1.02
1983792--1983817	2	13.0	2	100	0	52	50	0	0	50	1.00
1986556--1986625	31	2.3	31	82	9	90	41	4	1	52	1.30
1987305--1987341	2	19.0	2	88	5	58	54	0	0	45	1.00
1987524--1987568	17	2.8	16	83	12	65	57	0	0	42	0.98
1987524--1987568	9	5.4	9	77	20	53	57	0	0	42	0.98
1987915--1987944	2	15.0	2	92	0	51	50	3	0	46	1.18
1994431--1994545	54	2.1	54	95	1	205	39	3	5	52	1.41
1995678--1996211	267	2.0	267	94	0	933	25	25	15	34	1.95
1997557--1997646	43	2.1	43	93	0	153	53	12	20	14	1.72
2001475--2001535	22	2.8	22	80	7	72	54	0	0	45	1.00
2001491--2001535	21	2.2	20	84	4	54	53	0	0	46	1.00
2001774--2001809	18	2.0	18	89	10	56	47	0	2	50	1.15
2002330--2002376	21	2.2	20	82	10	58	59	8	6	25	1.50
2010094--2010134	3	13.3	3	94	5	73	31	0	0	68	0.90
2010878--2010916	18	2.0	20	90	9	64	61	0	5	33	1.18
2011857--2011900	9	5.0	9	80	5	54	75	2	0	22	0.92
2011870--2011954	36	2.4	36	80	2	91	62	2	0	35	1.08
2011868--2011943	19	4.1	19	65	13	50	60	2	0	36	1.11
2011972--2012019	23	2.1	23	85	11	64	6	18	0	75	1.01
2012404--2012580	93	1.9	94	94	1	311	33	16	10	39	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2020147--2020507	181	2.0	181	100	0	722	29	18	18	32	1.95
2021198--2021238	21	2.0	21	85	9	57	43	0	4	51	1.23
2025522--2025559	17	2.2	17	86	9	51	81	7	2	7	0.96
2026128--2026200	24	3.1	24	78	18	82	61	0	0	38	0.96
2030984--2031015	4	8.0	4	100	0	64	75	0	0	25	0.81
2031170--2031250	32	2.5	32	84	9	103	48	0	1	50	1.08
2031256--2031302	18	2.6	19	76	10	53	48	0	2	48	1.13
2032504--2032607	11	9.5	11	72	22	62	58	0	1	39	1.09
2032507--2032550	14	3.1	14	80	6	54	59	0	0	40	0.98
2032510--2032612	19	5.2	19	66	23	59	57	0	1	40	1.10
2035870--2036050	34	5.4	33	82	5	220	43	26	6	23	1.78
2035869--2036051	67	2.7	67	87	3	251	43	26	6	23	1.78
2035870--2036050	100	1.8	101	90	1	292	43	26	6	23	1.78
2038762--2038816	19	2.9	19	83	0	74	36	18	18	27	1.94
2039124--2039324	34	6.1	34	72	15	145	42	20	5	30	1.75
2040299--2040348	23	2.1	24	88	3	75	50	0	2	48	1.12
2040493--2040521	2	14.5	2	100	0	58	51	0	0	48	1.00
2040708--2040786	12	6.2	12	75	18	54	54	0	0	45	0.99
2040727--2040782	2	30.0	2	75	13	57	53	0	0	46	1.00
2040746--2040813	5	13.4	5	80	9	59	42	0	0	57	0.98
2041065--2041369	150	2.0	150	89	2	472	39	4	9	46	1.59
2054424--2054453	15	1.9	16	93	6	53	36	0	0	63	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2054467--2054663	55	3.5	56	72	13	177	38	2	8	51	1.45
2054466--2054698	115	2.0	116	94	0	405	36	2	7	52	1.44
2054489--2054724	115	2.1	115	88	1	348	38	3	6	51	1.45
2054837--2054924	17	4.3	21	65	22	53	44	5	1	48	1.33
2054855--2054888	17	2.0	17	94	0	59	41	8	0	50	1.34
2055291--2055346	20	2.8	20	80	2	67	53	1	0	44	1.11
2059967--2060010	22	2.0	22	86	0	61	65	6	0	27	1.17
2071067--2071199	24	5.4	25	68	24	61	39	0	0	60	0.97
2071092--2071198	51	2.1	52	81	6	121	38	0	0	61	0.96
2071146--2071199	13	4.4	13	76	19	62	31	0	0	68	0.90
2071059--2071203	11	13.1	11	69	19	61	38	0	0	61	0.96
2071860--2071889	2	15.0	2	92	0	51	3	50	0	46	1.18
2074489--2074515	2	13.5	2	100	0	54	51	0	0	48	1.00
2075717--2075768	23	2.2	25	82	6	63	57	3	0	38	1.17
2077036--2077077	22	1.9	22	85	0	57	45	0	0	54	0.99
2077034--2077088	28	2.0	28	85	0	74	47	0	0	52	1.00
2077073--2077109	18	2.0	19	89	5	58	56	0	0	43	0.99
2077295--2077321	14	1.9	14	100	0	54	18	0	0	81	0.69
2077761--2077788	2	14.0	2	100	0	56	50	0	0	50	1.00
2080450--2080488	13	3.3	13	73	26	50	58	0	0	41	0.98
2081294--2081333	2	20.0	2	100	0	80	50	0	0	50	1.00
2082374--2082426	24	2.2	24	90	3	81	50	1	5	41	1.36
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2083051--2083092	21	2.0	21	85	4	57	16	0	2	80	0.81
2083050--2083093	10	4.3	10	80	5	52	15	0	2	81	0.78
2091637--2091661	12	2.1	12	100	0	50	52	40	0	8	1.31
2095723--2095779	22	2.8	19	75	15	53	59	3	0	36	1.14
2097545--2097608	32	2.0	33	87	3	94	45	1	1	51	1.20
2097535--2097602	16	4.2	17	70	20	56	42	1	1	54	1.18
2097645--2097688	20	2.2	20	84	15	56	40	6	0	52	1.28
2098132--2098178	2	23.5	2	91	0	76	51	0	4	44	1.21
2101565--2101596	2	16.0	2	93	0	55	53	0	0	46	1.00
2105652--2105694	23	1.9	23	85	4	61	53	0	0	46	1.00
2106997--2107033	16	2.3	16	90	0	56	86	0	10	2	0.67
2111715--2111753	16	2.4	16	86	4	51	43	0	0	56	0.99
2112934--2112971	17	2.2	18	85	4	51	68	0	0	31	0.90
2114989--2115030	23	1.9	21	85	9	57	35	0	2	61	1.09
2115042--2115076	14	2.4	15	85	9	54	57	2	0	40	1.14
2127107--2127158	26	2.0	26	85	10	72	63	0	1	34	1.06
2127107--2127157	15	3.8	14	76	23	56	62	0	1	35	1.06
2127095--2127159	25	2.6	24	77	18	69	60	0	4	35	1.18
2127481--2127506	9	2.9	9	100	0	52	34	7	11	46	1.69
2127897--2127935	20	2.0	20	85	5	53	58	0	0	41	0.98
2128940--2128983	22	2.0	22	82	8	54	52	2	6	38	1.41
2129022--2129066	16	2.8	16	82	0	54	57	6	2	33	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2132344--2132422	34	2.3	35	79	12	85	49	0	0	50	1.00
2132375--2132473	38	2.6	38	78	15	98	51	0	0	48	1.00
2132506--2132540	16	2.1	16	89	5	52	60	0	0	40	0.97
2132494--2132560	29	2.4	28	78	9	82	53	0	0	46	1.00
2134634--2134661	2	14.0	2	100	0	56	0	50	0	50	1.00
2135927--2135956	7	4.3	7	100	0	60	30	0	0	70	0.88
2141847--2141872	13	2.0	13	100	0	52	23	23	23	30	1.99
2142726--2142769	21	2.2	20	83	4	52	50	2	0	47	1.13
2143523--2143554	14	2.3	14	94	0	55	37	0	0	62	0.95
2143942--2144021	42	1.9	41	82	12	101	58	2	0	38	1.11

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