genome.fa.s1.2.7.7.80.10.50.1000.4.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: chr1
Parameters: 2 7 7 80 10 50 1000
Length:  37323695

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   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   

This is table  4  of  93  ( 11113 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)
1707595--1707644	23	2.2	23	92	0	82	4	4	16	76	1.10
1707836--1707883	21	2.4	19	83	13	60	16	2	2	79	0.93
1707835--1707884	22	2.3	22	86	10	68	18	2	2	78	0.95
1713047--1713108	9	7.2	9	71	10	58	16	45	4	33	1.68
1713039--1713078	18	2.2	18	86	0	53	10	47	7	35	1.65
1713422--1713459	15	2.5	15	91	0	58	10	44	2	42	1.52
1738227--1738277	18	2.8	18	84	0	66	23	72	3	0	1.01
1738240--1738273	12	2.8	12	95	0	59	17	79	2	0	0.86
1741754--1741791	14	2.7	14	91	0	58	57	10	15	15	1.64
1746703--1746754	25	2.0	26	88	3	79	55	7	7	28	1.56
1752777--1752801	9	2.8	9	100	0	50	32	44	24	0	1.54
1753603--1753644	20	2.2	19	86	4	57	52	9	9	28	1.65
1767193--1767233	2	20.5	2	100	0	82	51	0	0	48	1.00
1768131--1768178	18	2.7	18	81	12	55	81	2	16	0	0.79
1768133--1768166	13	2.6	13	86	13	52	85	2	11	0	0.71
1782942--1783018	3	23.7	3	71	23	50	1	32	7	58	1.35
1782942--1783018	24	3.3	23	87	12	106	1	32	7	58	1.35
1782899--1783029	21	5.9	21	75	18	106	1	33	9	55	1.41
1782949--1783045	24	4.0	24	76	6	88	1	36	8	54	1.37
1782943--1783047	21	4.6	21	70	21	59	0	35	7	56	1.34
1797609--1797648	20	2.0	20	100	0	80	25	25	15	35	1.94
1822168--1822212	22	2.0	22	86	0	63	17	22	33	26	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1824341--1824388	19	2.5	19	83	6	62	39	0	8	52	1.32
1836743--1836848	38	2.7	38	85	8	133	63	6	5	24	1.41
1840080--1840106	13	2.1	13	100	0	54	22	0	37	40	1.54
1844322--1844371	2	25.0	2	100	0	100	50	0	0	50	1.00
1844392--1844442	2	25.5	2	100	0	102	49	0	0	50	1.00
1846700--1846938	118	2.0	118	96	1	444	40	12	15	31	1.84
1847536--1847581	23	2.0	23	83	8	58	43	0	8	47	1.34
1849748--1849783	15	2.4	15	100	0	72	25	30	0	44	1.54
1852174--1852290	14	8.1	14	68	16	53	64	0	4	30	1.12
1852218--1852291	31	2.5	29	81	12	96	64	0	5	29	1.15
1870892--1870916	5	5.0	5	100	0	50	80	0	0	20	0.72
1877707--1877772	29	2.3	28	75	17	64	62	0	13	24	1.31
1877948--1877981	5	6.6	5	89	3	50	79	2	17	0	0.86
1878724--1878752	3	9.7	3	100	0	58	31	0	0	68	0.89
1897069--1897093	10	2.5	10	100	0	50	28	0	16	56	1.41
1901884--1901925	2	21.0	2	100	0	84	50	0	0	50	1.00
1902060--1902101	21	2.0	21	100	0	84	33	14	23	28	1.94
1906679--1906725	14	3.3	15	85	8	71	48	0	0	51	1.00
1906666--1906779	29	4.2	28	73	17	89	42	0	0	57	0.98
1907240--1907312	22	3.5	20	76	17	69	45	0	0	54	0.99
1907248--1907299	25	2.0	26	96	3	97	42	0	0	57	0.98
1907285--1907315	16	1.9	16	100	0	62	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1907240--1907321	19	4.0	20	73	19	71	46	0	0	53	1.00
1911300--1911428	23	5.7	23	77	5	109	35	26	10	27	1.90
1911502--1911556	22	2.5	22	88	5	76	47	21	7	23	1.76
1911474--1911609	22	6.3	22	69	10	73	45	22	10	21	1.82
1911504--1911607	43	2.4	43	83	1	118	45	23	9	22	1.81
1911474--1911609	65	2.1	65	82	5	159	45	22	10	21	1.82
1915308--1915379	13	5.2	13	73	15	56	62	1	0	36	1.04
1915310--1915374	11	6.2	10	72	13	51	64	1	0	33	1.03
1919049--1919109	32	1.9	32	89	0	95	36	14	9	39	1.80
1924909--1924943	6	5.8	6	96	0	61	51	11	37	0	1.38
1928486--1928526	2	20.5	2	94	0	73	51	0	0	48	1.00
1934844--1934882	18	2.2	18	90	9	62	46	2	2	48	1.29
1934958--1935006	14	3.4	14	75	13	55	63	14	0	22	1.30
1935290--1935359	22	3.0	22	76	15	77	51	0	0	48	1.00
1935294--1935355	8	7.6	8	72	16	56	53	0	0	46	1.00
1940497--1940533	11	3.2	12	88	7	51	86	0	13	0	0.57
1948751--1948800	6	8.3	6	80	8	57	16	64	2	18	1.39
1959681--1959746	3	22.0	3	79	0	51	36	1	37	24	1.65
1959685--1959743	15	3.9	15	78	8	66	37	1	38	22	1.64
1962309--1962377	36	1.9	36	82	5	86	15	28	14	40	1.87
1965687--1965763	38	2.0	38	100	0	154	38	20	7	32	1.81
1983163--1983190	8	3.5	8	100	0	56	21	0	0	78	0.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1985246--1985341	48	2.0	48	91	0	156	51	15	14	18	1.77
1986265--1986293	2	14.5	2	100	0	58	48	0	0	51	1.00
1986361--1986402	20	2.0	20	86	4	57	66	9	11	11	1.44
1987518--1987551	1	34.0	1	87	0	50	94	0	5	0	0.32
1987566--1987612	10	4.7	10	79	10	51	65	4	29	0	1.11
1991928--1991959	2	16.0	2	93	0	55	50	3	0	46	1.17
1993616--1993655	21	1.9	21	89	0	62	52	40	5	2	1.37
1995305--1995358	25	2.1	25	83	10	65	50	12	9	27	1.71
2005160--2005326	81	2.0	82	96	1	309	29	13	16	40	1.87
2018023--2018052	4	7.5	4	100	0	60	50	0	23	26	1.50
2020249--2020422	85	2.0	87	87	4	255	47	15	14	21	1.82
2024389--2024425	2	19.0	2	84	15	51	2	51	0	45	1.15
2024466--2024502	2	19.0	2	84	15	51	2	51	0	45	1.15
2024372--2024524	77	2.0	76	100	0	297	16	33	7	40	1.78
2042475--2042504	2	15.0	2	92	0	51	53	0	46	0	1.00
2042475--2042511	12	3.1	12	92	0	56	54	0	45	0	1.00
2051644--2051715	30	2.4	30	90	0	117	31	5	8	54	1.54
2060383--2060483	46	2.2	46	85	1	130	42	24	19	12	1.87
2070652--2070685	12	2.8	12	90	0	50	0	41	5	52	1.25
2070649--2070685	16	2.3	16	95	0	65	0	43	5	51	1.24
2075971--2076034	21	3.0	21	73	13	69	32	10	43	12	1.77
2086357--2086794	217	2.0	218	88	2	648	30	13	23	32	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2086997--2087218	65	3.4	64	85	4	259	34	14	19	31	1.92
2087494--2087562	35	2.0	35	85	0	93	27	14	24	33	1.94
2093815--2093925	5	22.4	5	65	12	50	27	2	0	69	1.02
2093851--2093928	15	5.6	14	72	18	65	26	1	0	71	0.93
2093863--2093936	34	2.2	33	83	13	89	29	1	0	68	0.97
2113066--2113153	44	2.0	44	97	0	167	46	18	17	18	1.84
2118185--2118236	28	1.9	27	88	7	79	63	3	1	30	1.23
2122550--2122614	33	2.0	33	84	3	87	53	0	6	40	1.26
2151097--2151129	16	2.0	17	88	5	50	63	0	30	6	1.18
2151093--2151121	13	2.3	13	94	5	51	65	0	31	3	1.09
2170765--2170818	26	2.1	25	86	3	72	57	0	0	42	0.98
2171166--2171195	14	2.1	14	93	0	51	60	0	0	40	0.97
2178457--2178546	34	2.6	34	92	0	144	21	13	14	51	1.76
2187618--2187644	2	13.5	2	100	0	54	51	0	0	48	1.00
2204893--2204965	36	2.0	36	97	0	137	31	28	20	19	1.97
2217017--2217068	23	2.3	22	75	12	52	11	7	7	73	1.26
2221677--2221770	28	3.4	28	79	5	84	47	1	6	44	1.35
2221703--2221796	31	3.2	28	76	14	84	42	3	7	46	1.47
2228575--2228620	23	2.1	21	84	11	58	34	4	15	45	1.66
2232180--2232205	2	13.0	2	100	0	52	50	0	0	50	1.00
2240196--2240241	7	5.9	8	77	12	51	26	2	0	71	0.97
2240206--2240241	15	2.4	15	95	0	63	25	0	0	75	0.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2240225--2240279	18	3.1	18	74	12	51	40	1	1	56	1.21
2240213--2240280	17	4.1	16	70	18	50	33	1	1	63	1.13
2240501--2240536	18	2.0	18	89	10	56	22	0	0	77	0.76
2240957--2241035	37	2.1	37	84	9	99	0	31	2	65	1.06
2240921--2241149	102	2.2	106	82	8	272	2	32	4	60	1.32
2241079--2241145	9	7.6	9	71	15	59	0	23	2	73	0.97
2241093--2241160	15	4.4	16	72	9	52	0	27	2	69	1.03
2241066--2241166	53	1.9	53	89	0	157	0	28	3	67	1.09
2241059--2241153	21	4.5	21	69	20	65	0	27	2	70	0.98
2241114--2241160	21	2.2	21	81	7	60	0	29	0	70	0.88

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   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93