genome.fa.s38.2.7.7.80.10.50.1000.14.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: Scaffold38
Parameters: 2 7 7 80 10 50 1000
Length:  2073527

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   

This is table  14  of  15  ( 1750 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)
1879672--1879703	3	10.7	3	100	0	64	68	0	0	31	0.90
1880210--1880264	19	2.8	18	82	15	65	58	1	0	40	1.09
1880825--1880864	2	19.5	2	94	5	71	50	0	2	47	1.14
1881144--1881182	19	2.2	19	90	9	64	46	0	2	51	1.14
1881144--1881195	21	2.7	21	83	13	60	44	0	1	53	1.11
1881192--1881236	21	2.1	22	88	12	67	60	0	0	40	0.97
1884225--1884480	129	2.0	130	93	0	442	33	17	14	34	1.90
1884772--1884810	4	10.2	4	83	10	55	71	0	28	0	0.86
1884896--1884926	3	10.3	3	100	0	62	32	0	0	67	0.91
1885842--1885889	2	24.0	2	100	0	96	50	0	50	0	1.00
1894716--1894740	2	12.5	2	100	0	50	52	0	48	0	1.00
1894941--1894968	3	9.3	3	100	0	56	67	0	0	32	0.91
1897782--1897825	17	2.6	16	79	10	52	47	0	2	50	1.13
1898144--1898181	16	2.2	18	90	9	62	28	0	0	71	0.87
1898129--1898182	28	2.0	26	89	7	81	29	0	0	70	0.88
1898519--1898567	19	2.6	19	75	12	55	22	6	0	71	1.08
1898791--1898851	16	3.9	16	80	6	63	68	0	3	27	1.05
1899558--1899590	13	2.4	14	90	5	50	69	0	3	27	1.03
1900508--1900571	19	3.3	20	80	6	69	40	0	0	59	0.97
1902348--1902377	3	10.0	3	100	0	60	66	0	0	33	0.92
1904424--1904478	28	2.0	28	92	0	92	38	10	5	45	1.63
1904954--1904978	3	8.3	3	100	0	50	32	0	0	68	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1905458--1905564	54	2.0	54	94	3	189	22	17	14	45	1.84
1906129--1906174	20	2.4	19	85	3	65	67	2	2	28	1.14
1906139--1906181	20	2.1	20	86	4	59	72	0	2	25	0.97
1906533--1906570	16	2.3	17	95	4	69	44	0	0	55	0.99
1906532--1906575	15	2.9	15	83	12	54	45	0	0	54	0.99
1906772--1906802	14	2.1	15	94	5	55	61	0	0	38	0.96
1906795--1906862	29	2.3	29	76	14	68	57	1	1	39	1.17
1907737--1907798	31	2.0	31	93	6	108	35	6	6	51	1.53
1908814--1908852	15	2.6	15	83	0	51	38	2	0	58	1.12
1909754--1909788	17	2.0	18	88	5	54	77	0	0	22	0.78
1909749--1909815	18	3.9	17	79	11	66	70	1	0	28	0.96
1909750--1909830	27	3.0	27	82	12	87	69	3	0	27	1.05
1912097--1912175	36	2.1	37	84	13	101	56	5	1	36	1.29
1912800--1912835	17	2.1	17	89	0	54	44	0	2	52	1.15
1913543--1913839	98	3.0	97	88	4	445	33	30	11	25	1.90
1915747--1915796	11	4.4	12	78	12	61	60	0	0	40	0.97
1915751--1915796	15	2.8	16	74	25	51	60	0	0	39	0.97
1915787--1915840	21	2.7	19	75	8	54	53	1	0	44	1.11
1916379--1916428	9	5.8	9	77	13	52	66	0	0	34	0.92
1916377--1916427	25	2.1	24	85	10	68	66	0	0	33	0.92
1916909--1916936	2	14.0	2	100	0	56	50	0	0	50	1.00
1917461--1917497	18	2.1	19	85	10	51	67	8	10	13	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1922777--1922802	3	8.7	3	100	0	52	69	0	0	30	0.89
1923061--1923101	22	1.9	22	90	5	66	46	7	0	46	1.30
1924245--1924282	20	2.0	19	90	10	60	36	0	2	60	1.11
1924251--1924289	19	2.0	20	90	5	62	38	0	5	56	1.22
1924670--1924756	23	3.7	23	81	7	95	48	1	0	50	1.08
1925267--1925323	28	2.1	28	87	9	82	57	1	0	40	1.09
1927522--1927558	10	3.9	10	79	13	51	78	0	21	0	0.75
1928801--1928881	19	4.5	19	67	17	64	43	0	3	53	1.18
1928810--1928874	34	1.9	34	87	0	94	40	0	4	55	1.21
1929154--1929182	2	14.5	2	100	0	58	51	0	0	48	1.00
1931770--1931839	31	2.3	31	87	5	97	48	0	1	50	1.09
1931770--1931839	16	4.5	15	81	10	79	48	0	1	50	1.09
1932189--1932233	14	3.0	15	80	9	56	42	0	2	55	1.12
1932296--1932340	20	2.1	22	84	8	58	57	4	2	35	1.31
1932267--1932382	62	1.9	61	91	3	189	51	6	3	37	1.46
1933085--1933122	2	19.0	2	94	0	67	47	0	0	52	1.00
1934379--1934433	19	2.9	19	70	20	51	65	0	0	34	0.93
1934390--1934489	33	3.0	33	74	10	89	58	0	0	42	0.98
1934379--1934471	40	2.4	39	82	7	109	61	0	0	38	0.96
1934400--1934489	20	4.4	22	67	25	63	56	0	0	43	0.99
1935746--1935787	20	2.0	22	90	9	70	69	0	0	30	0.89
1939175--1939211	13	2.8	13	87	0	56	37	0	0	62	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1939502--1939539	13	3.1	13	88	7	53	39	0	0	60	0.97
1940414--1940461	25	2.0	25	84	8	64	64	0	2	33	1.05
1940943--1940972	2	15.0	2	100	0	60	50	0	0	50	1.00
1941612--1941663	24	2.1	25	86	10	72	32	0	0	67	0.91
1941612--1941654	13	3.5	12	87	12	61	30	0	0	69	0.88
1941603--1941647	18	2.7	16	80	12	54	31	0	2	66	1.04
1941626--1941662	13	2.8	13	87	0	56	32	0	0	67	0.91
1942043--1942104	5	13.2	5	74	19	62	41	0	0	58	0.98
1943386--1943546	8	19.6	8	66	25	54	38	0	0	60	1.06
1943379--1943415	16	2.3	16	95	0	65	32	2	5	59	1.34
1943386--1943475	6	15.5	6	68	23	59	35	0	1	63	1.02
1943393--1943469	25	3.0	25	83	12	93	36	0	1	62	1.04
1943431--1943527	32	3.0	31	77	15	99	42	1	0	56	1.06
1943466--1943558	17	5.6	16	69	23	59	40	1	0	58	1.05
1943404--1943557	8	18.5	8	68	22	61	38	0	0	60	1.02
1946114--1946165	24	2.2	24	85	0	68	51	0	1	46	1.12
1946127--1946186	16	3.5	17	79	6	68	53	0	0	46	1.00
1946127--1946196	34	2.1	34	84	7	90	55	0	0	44	0.99
1946157--1946181	13	1.9	13	100	0	50	56	0	0	44	0.99
1948197--1948246	24	2.0	25	84	3	66	38	6	0	56	1.24
1949140--1949218	31	2.7	26	77	22	86	43	0	0	56	0.99
1949144--1949183	20	2.0	20	85	9	55	45	0	0	55	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1949153--1949207	16	3.6	16	68	7	51	47	0	0	52	1.00
1949553--1949686	64	2.1	63	84	1	169	44	11	10	33	1.74
1951040--1951092	21	2.6	21	80	11	58	56	0	0	43	0.99
1951724--1951791	33	2.1	32	91	2	109	57	0	0	42	0.98
1952417--1952456	11	3.9	10	84	15	55	77	2	2	17	0.99
1963523--1963570	3	16.0	3	86	0	69	35	2	2	60	1.20
1964054--1964088	16	2.2	16	90	5	54	74	8	0	17	1.06
1964028--1964106	26	2.9	26	72	14	61	64	10	1	24	1.32
1964163--1964203	18	2.3	18	87	8	57	43	14	2	39	1.59
1964566--1964617	24	2.1	24	85	3	68	65	9	7	17	1.45
1969914--1969949	18	1.9	18	88	5	54	41	0	0	58	0.98
1970320--1970376	20	2.8	20	71	10	62	40	0	0	59	0.97
1970320--1970416	40	2.5	38	80	12	101	40	1	0	58	1.05
1970331--1970437	33	3.3	31	81	12	108	41	0	0	57	1.12
1971305--1971348	2	22.0	2	100	0	88	50	0	50	0	1.00
1973722--1973797	23	3.5	23	68	14	79	17	10	19	52	1.73
1973712--1973796	42	2.0	42	100	0	170	21	11	18	48	1.80
1977176--1977204	5	5.8	5	100	0	58	17	0	0	82	0.66
1978006--1978059	10	5.4	9	79	18	54	27	0	1	70	0.98
1978015--1978084	24	3.0	22	82	10	86	31	1	0	67	1.00
1977991--1978059	31	2.2	32	82	15	90	30	0	2	66	1.06
1977989--1978076	11	7.8	11	71	18	65	30	1	2	65	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1978034--1978082	17	2.9	17	80	20	59	32	2	0	65	1.04
1978337--1978362	2	13.0	2	100	0	52	50	0	0	50	1.00
1978844--1978878	14	2.5	14	86	13	54	31	0	0	68	0.90
1978977--1979024	19	2.5	19	80	10	53	39	0	0	60	0.97
1980306--1980332	4	6.8	4	100	0	54	22	0	0	77	0.76
1989417--1989442	2	13.0	2	100	0	52	50	0	50	0	1.00
1992405--1992435	12	2.6	12	94	0	53	29	9	0	61	1.28
1998279--1998328	7	6.9	7	78	17	57	42	0	0	58	0.98
1998292--1998334	14	2.9	14	80	19	52	44	0	0	55	0.99
1998731--1998758	2	14.0	2	100	0	56	50	0	0	50	1.00

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15