genome.fa.s3.2.7.7.80.10.50.1000.14.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: Scaffold3
Parameters: 2 7 7 80 10 50 1000
Length:  6198200

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   

This is table  14  of  32  ( 3795 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)
2018046--2018088	12	3.7	11	78	9	50	37	2	2	58	1.24
2018358--2018394	2	18.5	2	100	0	74	51	0	0	48	1.00
2020619--2020660	16	2.6	16	88	0	66	38	0	4	57	1.20
2020783--2020825	21	2.0	22	86	4	61	34	4	0	60	1.17
2021632--2021679	22	2.2	22	92	0	78	37	6	0	56	1.25
2022930--2023022	44	2.2	41	77	11	100	53	0	0	46	1.00
2023261--2023292	3	10.7	3	100	0	64	31	0	0	68	0.90
2023841--2023900	30	2.0	29	84	9	77	38	0	1	60	1.07
2024292--2024361	19	3.6	19	79	7	79	40	0	0	60	0.97
2024311--2024367	26	2.1	27	81	9	64	43	0	0	56	0.99
2025806--2025833	6	4.7	6	100	0	56	85	0	14	0	0.59
2029358--2029403	2	23.0	2	90	0	74	50	4	0	45	1.21
2034612--2034645	14	2.4	14	90	9	52	55	0	0	44	0.99
2034631--2034689	30	2.0	30	83	3	75	33	0	1	64	1.04
2037064--2037106	21	2.0	21	90	0	68	46	4	18	30	1.69
2039066--2039223	84	1.9	84	84	2	210	38	12	4	44	1.62
2040457--2040490	6	5.7	6	96	0	50	23	35	23	17	1.95
2045915--2045956	21	2.0	20	86	4	57	42	0	0	57	0.99
2046471--2046501	2	16.0	2	93	6	55	48	0	0	51	1.00
2051015--2051083	23	3.1	22	71	25	56	47	0	0	52	1.00
2051022--2051083	23	2.9	21	73	21	65	50	0	0	50	1.00
2051571--2051606	15	2.4	16	90	9	58	66	0	0	33	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2053336--2053363	2	14.0	2	100	0	56	50	0	0	50	1.00
2057427--2057482	21	2.6	22	78	10	62	41	0	1	57	1.09
2057427--2057479	23	2.4	22	81	6	63	41	0	1	56	1.10
2059198--2059231	6	5.7	6	85	0	50	20	0	2	76	0.92
2062805--2062847	19	2.3	19	87	0	59	53	2	0	44	1.13
2063996--2064031	3	12.0	3	87	0	54	36	0	2	61	1.11
2064378--2064412	14	2.4	14	95	4	61	34	14	8	42	1.76
2065351--2065375	2	12.5	2	100	0	50	48	0	0	52	1.00
2066100--2066139	19	2.1	19	95	0	71	55	0	0	45	0.99
2066695--2066741	20	2.3	21	79	17	55	34	0	2	63	1.06
2068322--2068358	3	12.7	3	94	5	67	32	0	0	67	0.91
2068659--2068689	2	15.5	2	100	0	62	51	0	0	48	1.00
2069551--2069630	12	6.7	12	75	0	61	11	6	56	26	1.58
2069551--2069624	18	4.1	18	78	3	78	12	6	56	24	1.59
2070825--2070895	15	5.1	14	75	19	69	59	0	0	40	0.98
2070829--2070894	19	3.2	21	70	27	61	59	0	0	40	0.98
2072175--2072213	18	2.0	20	90	9	64	53	0	0	46	1.00
2074013--2074041	2	14.5	2	100	0	58	51	0	0	48	1.00
2074204--2074272	27	2.7	24	77	16	66	55	0	1	43	1.08
2076239--2076331	43	2.1	43	90	2	141	30	25	11	32	1.92
2076432--2076464	2	16.5	2	100	0	66	51	0	0	48	1.00
2078470--2078533	25	2.7	25	79	15	73	42	0	0	57	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2079346--2079395	25	2.2	22	79	13	57	62	0	0	38	0.96
2081466--2081506	2	20.5	2	100	0	82	51	0	0	48	1.00
2084397--2084480	21	4.0	21	75	9	91	40	5	5	47	1.52
2084385--2084465	41	2.0	41	92	0	135	45	4	6	43	1.50
2087261--2087297	9	4.0	9	96	3	65	0	13	0	86	0.57
2089581--2089607	12	2.2	12	100	0	54	48	18	7	25	1.74
2090650--2090682	6	5.5	6	96	0	57	0	12	33	54	1.37
2092677--2092733	21	2.9	18	78	16	60	42	1	0	56	1.10
2092691--2092735	21	2.1	22	87	4	65	44	0	0	55	0.99
2095007--2095124	61	1.9	61	92	0	200	49	1	10	38	1.47
2096124--2096170	15	2.8	18	81	15	57	70	0	12	17	1.17
2098029--2098061	17	2.0	16	94	5	57	51	0	6	42	1.26
2098875--2098919	8	6.0	8	80	12	51	62	2	0	35	1.08
2098878--2098920	22	2.0	22	90	9	70	65	2	0	32	1.06
2099022--2099046	2	12.5	2	100	0	50	48	0	0	52	1.00
2113191--2113222	2	16.0	2	100	0	64	50	0	0	50	1.00
2113808--2114150	171	2.0	171	100	0	686	37	16	18	27	1.92
2118824--2118854	15	2.1	15	93	0	53	48	0	0	51	1.00
2120259--2120311	20	2.5	23	74	22	62	58	3	0	37	1.16
2120559--2120613	27	2.2	25	84	12	69	67	0	1	30	1.01
2122013--2122106	22	4.1	21	71	20	73	42	3	1	53	1.24
2123161--2123199	18	2.2	17	86	4	51	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)
2123442--2123504	3	21.3	3	93	3	101	66	3	0	30	1.07
2131321--2131373	23	2.3	23	81	9	65	45	0	0	54	0.99
2137285--2137312	3	9.3	3	100	0	56	67	0	0	32	0.91
2137311--2137338	3	9.3	3	100	0	56	32	0	0	67	0.91
2138234--2138258	2	12.5	2	100	0	50	48	0	0	52	1.00
2139467--2139515	21	2.3	21	85	3	62	67	0	0	32	0.91
2139677--2139734	5	11.6	5	74	18	50	44	0	0	55	0.99
2139664--2139743	24	3.3	25	79	19	73	50	0	0	50	1.00
2139739--2139781	20	2.1	21	86	4	61	58	2	2	37	1.24
2141559--2141601	17	2.5	18	81	11	54	41	0	0	58	0.98
2142395--2142436	21	1.9	21	90	9	66	52	2	0	45	1.13
2143463--2143499	2	18.5	2	100	0	74	51	0	48	0	1.00
2147868--2147912	17	2.5	18	85	7	56	57	2	0	40	1.11
2154207--2154255	2	24.5	2	100	0	98	48	0	51	0	1.00
2155086--2155122	2	18.5	2	94	0	65	48	0	2	48	1.15
2156515--2156540	3	8.7	3	100	0	52	30	0	0	69	0.89
2161710--2161760	25	2.0	25	92	0	84	21	15	33	29	1.94
2162862--2162889	13	2.2	13	100	0	56	53	0	7	39	1.28
2163153--2163187	2	17.5	2	93	0	61	51	2	0	45	1.16
2163745--2163774	4	7.5	4	92	0	51	26	0	0	73	0.84
2164133--2164157	13	1.9	13	100	0	50	48	0	0	52	1.00
2164725--2164756	7	4.7	7	92	7	57	15	40	15	28	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2164725--2164756	13	2.4	14	94	5	57	15	40	15	28	1.88
2165882--2165925	2	21.5	2	90	4	70	45	0	4	50	1.22
2167243--2167270	2	14.0	2	100	0	56	50	0	50	0	1.00
2170707--2170778	35	2.1	35	100	0	144	61	16	13	8	1.56
2172246--2172276	2	15.5	2	93	0	53	51	45	0	3	1.17
2175953--2176431	233	2.1	233	98	0	931	28	24	9	37	1.86
2185423--2185473	17	3.1	17	78	18	54	37	0	3	58	1.16
2185616--2185640	6	4.2	6	100	0	50	20	0	0	80	0.72
2185884--2185948	34	1.9	33	84	9	87	46	3	1	49	1.27
2185932--2185961	14	2.1	14	93	0	51	60	3	0	36	1.14
2186225--2186335	37	3.1	36	77	10	113	53	0	0	46	1.00
2186488--2186605	11	11.5	11	66	20	58	61	0	1	37	1.07
2186530--2186620	29	3.1	29	77	12	96	60	0	1	38	1.04
2186488--2186625	35	3.9	35	72	15	92	60	0	1	37	1.06
2186550--2186616	31	2.0	35	83	11	88	58	0	1	40	1.07
2186504--2186625	11	11.5	11	65	25	50	61	0	0	37	1.02
2188271--2188338	18	3.9	17	77	7	57	47	0	1	51	1.09
2188418--2188468	20	2.5	21	84	9	61	54	1	0	43	1.11
2189228--2189315	24	3.7	23	71	21	65	56	1	1	40	1.14
2194745--2194776	2	16.0	2	100	0	64	50	0	0	50	1.00
2195444--2195476	2	16.5	2	100	0	66	0	48	0	51	1.00
2204085--2204930	215	4.0	215	83	5	1042	24	12	16	46	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2204114--2204928	431	1.9	429	85	6	1064	24	12	16	46	1.81
2206112--2206211	51	2.0	51	93	0	173	29	12	20	39	1.88
2214338--2214365	2	14.0	2	100	0	56	50	0	0	50	1.00
2214576--2214611	18	2.0	18	88	0	54	19	8	0	72	1.10
2217272--2217315	22	1.9	24	86	9	65	54	4	4	36	1.41
2217674--2217710	13	2.5	16	87	12	53	29	0	0	70	0.88
2218769--2218796	2	14.0	2	100	0	56	50	0	0	50	1.00
2220220--2220263	19	2.4	17	82	14	52	50	0	4	45	1.22
2220656--2220700	23	1.9	23	90	4	72	55	0	0	44	0.99
2226031--2226290	131	2.0	131	87	3	380	39	15	13	31	1.86

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