genome.fa.s54.2.7.7.80.10.50.1000.12.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: Scaffold54
Parameters: 2 7 7 80 10 50 1000
Length:  3629595

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   

This is table  12  of  20  ( 2342 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)
1933100--1933240	44	3.3	42	80	9	155	29	20	10	39	1.86
1933368--1933438	16	4.8	15	78	14	69	56	0	0	43	0.99
1933367--1933429	14	4.5	13	76	21	56	55	0	0	44	0.99
1933384--1933429	14	3.4	14	82	14	60	56	0	0	43	0.99
1933879--1933930	25	2.1	24	82	3	59	51	0	7	40	1.30
1934054--1934086	14	2.4	14	100	0	66	33	0	0	66	0.92
1934062--1934127	15	3.7	17	75	19	55	28	1	0	69	0.97
1934705--1934736	8	4.0	8	100	0	64	25	0	0	75	0.81
1938085--1938128	22	1.9	24	86	9	65	50	0	4	45	1.22
1939199--1939237	20	2.0	20	90	5	62	46	0	0	53	1.00
1940883--1940917	17	2.0	18	94	5	63	51	0	0	48	1.00
1941218--1941248	5	6.2	5	96	0	53	45	0	54	0	0.99
1941452--1941481	4	7.5	4	100	0	60	73	0	0	26	0.84
1942007--1942063	16	3.4	17	79	15	64	47	1	0	50	1.11
1942351--1942389	16	2.5	15	87	8	51	64	0	0	35	0.94
1942772--1942814	14	2.9	15	82	3	61	37	6	2	53	1.41
1945771--1945825	3	18.3	3	96	0	101	32	1	0	65	1.03
1948649--1948683	3	11.7	3	100	0	70	31	0	0	68	0.90
1953106--1953146	17	2.3	17	87	8	55	48	0	0	51	1.00
1953238--1953284	20	2.4	19	82	10	58	42	0	0	57	0.98
1953253--1953421	28	5.9	26	70	23	94	42	0	2	55	1.13
1953244--1953437	86	2.2	86	96	0	361	41	0	2	56	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1953254--1953374	5	23.0	5	69	18	68	42	0	2	55	1.13
1953440--1953480	16	2.6	16	85	11	57	63	0	0	36	0.95
1954423--1954476	12	4.5	12	79	4	56	50	0	1	48	1.11
1956921--1956953	17	1.9	17	88	11	50	63	0	6	30	1.18
1957848--1957929	43	1.9	43	89	0	128	41	8	4	45	1.56
1957992--1958142	43	3.8	43	68	22	121	39	11	3	46	1.56
1957999--1958117	39	3.2	38	66	24	90	41	10	2	46	1.51
1958012--1958125	35	3.1	34	70	18	104	40	11	2	45	1.54
1958033--1958091	31	1.9	31	85	0	82	35	13	5	45	1.66
1957992--1958134	74	1.9	74	95	0	259	39	11	2	46	1.55
1957816--1958260	216	2.1	207	89	4	676	43	9	3	42	1.55
1958191--1958259	35	2.0	35	85	5	95	44	5	2	46	1.42
1958261--1958331	32	2.2	32	89	2	106	53	5	4	36	1.44
1958166--1958439	140	2.0	140	94	0	485	50	6	2	40	1.43
1958410--1958452	20	2.2	20	84	12	54	48	0	0	51	1.00
1958519--1958576	25	2.3	25	90	0	89	55	3	0	41	1.17
1958529--1958595	25	2.8	25	90	4	102	55	2	0	41	1.15
1959677--1959724	17	2.9	17	81	3	53	33	6	2	58	1.35
1959712--1959767	24	2.3	23	84	6	67	33	8	0	57	1.30
1960526--1960620	5	18.2	5	68	15	50	46	0	0	53	1.00
1960522--1960629	37	3.2	32	77	16	96	43	0	0	55	1.06
1960485--1960587	16	6.5	16	70	16	72	36	0	1	60	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1960495--1960588	47	2.0	47	80	12	104	38	1	2	58	1.17
1960527--1960623	15	5.9	16	73	20	76	46	0	0	53	1.00
1961077--1961118	22	1.9	22	85	0	57	50	0	0	50	1.00
1961535--1961561	3	9.0	3	100	0	54	0	0	33	66	0.92
1979116--1979146	2	15.5	2	100	0	62	51	48	0	0	1.00
1980132--1980157	2	13.0	2	100	0	52	0	50	0	50	1.00
1984697--1984748	26	2.0	26	100	0	104	11	15	7	65	1.46
1989384--1989420	20	1.9	20	88	5	58	45	16	8	29	1.76
1993191--1993226	19	1.9	19	88	5	56	50	5	0	44	1.25
1993342--1993403	32	1.9	32	93	0	106	50	17	14	17	1.79
2002345--2002381	2	18.5	2	100	0	74	48	0	0	51	1.00
2003631--2003676	2	23.0	2	100	0	92	50	0	0	50	1.00
2004092--2004127	18	2.1	18	89	5	56	44	0	2	52	1.15
2008466--2008515	2	25.0	2	100	0	100	50	0	0	50	1.00
2011437--2011510	24	3.0	24	73	13	69	48	4	0	47	1.20
2012092--2012151	19	3.2	18	83	11	77	55	0	0	45	0.99
2012083--2012134	25	2.0	25	85	11	68	59	0	0	40	0.97
2012092--2012139	17	2.7	18	90	6	71	58	0	0	41	0.98
2012377--2012415	14	2.8	14	84	11	53	61	0	0	38	0.96
2012378--2012429	18	2.8	19	80	11	54	65	0	0	34	0.93
2012424--2012472	20	2.5	19	86	3	71	46	0	0	53	1.00
2013868--2013902	3	11.7	3	100	0	70	65	0	0	34	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2015091--2015123	16	2.1	16	88	11	50	33	6	0	60	1.21
2015091--2015132	22	1.9	22	85	0	57	35	4	0	59	1.19
2018633--2018717	44	2.0	42	90	6	136	23	8	16	51	1.71
2019552--2019579	3	9.3	3	100	0	56	32	0	0	67	0.91
2019570--2019629	31	1.9	31	83	6	77	41	5	1	51	1.33
2025291--2025329	16	2.4	17	86	4	53	43	2	0	53	1.14
2026041--2026103	17	3.6	17	77	12	65	44	0	0	55	0.99
2026070--2026100	15	2.0	16	93	6	55	35	0	0	64	0.94
2026833--2026870	16	2.4	16	82	8	51	57	2	0	39	1.12
2030160--2030236	38	2.0	38	92	0	127	31	19	10	38	1.85
2030991--2031296	152	2.0	152	97	0	576	24	17	18	39	1.92
2037745--2037786	20	2.1	20	100	0	84	23	19	19	38	1.93
2041664--2041697	17	1.9	18	94	5	61	88	0	11	0	0.52
2043049--2043089	20	2.0	22	85	9	59	63	0	0	36	0.95
2043387--2043477	27	3.4	29	73	21	74	53	3	0	42	1.17
2043462--2043512	25	2.0	26	84	3	68	45	1	0	52	1.12
2043491--2043530	21	1.9	21	85	10	55	40	0	0	60	0.97
2051473--2051505	2	16.5	2	100	0	66	51	0	0	48	1.00
2052741--2052885	72	2.0	72	100	0	290	47	17	5	28	1.70
2052986--2053039	27	2.0	27	89	10	83	51	7	3	37	1.48
2053022--2053085	26	2.5	26	80	10	78	46	3	1	48	1.27
2058172--2058213	2	21.0	2	95	0	75	47	2	50	0	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2059184--2059210	4	6.8	4	100	0	54	25	0	0	74	0.83
2062292--2062358	20	3.2	20	69	26	50	58	0	0	41	0.98
2065304--2065343	13	2.9	14	85	7	55	0	20	0	80	0.72
2065309--2065347	13	2.9	13	84	3	51	0	15	0	84	0.62
2067503--2067529	6	4.5	6	100	0	54	18	33	0	48	1.49
2068257--2068298	2	21.0	2	100	0	84	50	0	0	50	1.00
2073486--2073520	14	2.6	14	90	4	54	54	0	0	45	0.99
2074761--2074800	20	2.1	19	95	4	71	47	0	0	52	1.00
2075139--2075235	15	5.8	16	68	20	65	47	1	2	49	1.20
2075285--2075337	25	2.2	24	89	3	79	47	7	5	39	1.56
2076515--2076548	17	2.0	17	100	0	68	35	29	11	23	1.90
2078805--2078846	20	2.1	20	86	8	59	30	0	0	69	0.89
2079472--2079500	13	2.2	13	100	0	58	58	0	0	41	0.98
2080544--2080568	4	6.2	4	100	0	50	24	0	0	76	0.80
2081053--2081109	18	2.8	20	85	15	66	42	1	0	56	1.10
2082608--2082644	18	2.1	18	89	0	56	64	0	8	27	1.21
2085088--2085226	69	2.0	69	94	0	242	20	22	16	40	1.91
2090302--2090333	15	2.1	15	100	0	64	12	6	40	40	1.68
2091740--2091767	3	9.3	3	100	0	56	32	0	0	67	0.91
2092893--2092940	23	2.1	23	84	7	62	56	0	8	35	1.30
2094255--2094354	50	2.0	50	98	0	191	45	10	5	40	1.60
2094938--2094964	6	4.5	6	100	0	54	14	0	0	85	0.61
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2098099--2098158	18	3.5	18	73	19	65	48	0	0	51	1.00
2098098--2098173	33	2.3	33	88	4	109	50	0	0	50	1.00
2098679--2098721	16	2.7	15	92	7	68	48	0	2	48	1.14
2098679--2098743	10	6.3	10	70	12	51	50	0	1	47	1.10
2098676--2098746	20	3.5	20	76	18	58	49	0	1	49	1.09
2098692--2098774	36	2.4	36	81	15	95	46	0	4	48	1.23
2100041--2100067	4	6.8	4	100	0	54	51	22	0	25	1.48
2118136--2118182	10	4.9	10	79	10	62	21	51	27	0	1.48
2118136--2118182	6	8.5	6	77	17	57	21	51	27	0	1.48
2118136--2118182	16	3.2	16	77	22	66	21	51	27	0	1.48

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20