genome.fa.s8.2.7.7.80.10.50.1000.13.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: Scaffold8
Parameters: 2 7 7 80 10 50 1000
Length:  6381039

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   

This is table  13  of  33  ( 3942 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)
1729067--1729114	24	2.0	24	100	0	96	41	8	16	33	1.78
1729332--1729365	8	4.4	8	85	7	52	61	0	0	38	0.96
1729675--1729769	47	2.0	47	89	0	145	38	8	14	37	1.77
1732179--1732206	2	14.0	2	100	0	56	50	0	0	50	1.00
1732505--1732542	2	19.0	2	100	0	76	50	0	0	50	1.00
1732360--1732528	93	1.8	93	100	0	338	34	11	12	41	1.79
1732971--1733006	2	18.0	2	100	0	72	50	0	0	50	1.00
1732519--1734161	231	7.1	229	91	3	2558	28	16	15	40	1.88
1732517--1734163	241	7.1	231	91	4	2569	28	16	14	40	1.88
1733212--1733247	2	18.0	2	100	0	72	50	0	0	50	1.00
1734138--1734163	2	13.0	2	100	0	52	50	0	0	50	1.00
1734489--1734519	13	2.4	13	94	0	53	35	29	6	29	1.82
1734779--1734817	20	2.1	18	90	9	60	71	2	0	25	0.98
1739217--1739261	20	2.3	18	79	17	54	33	0	0	66	0.92
1739226--1739272	25	1.9	24	91	4	76	38	0	0	61	0.96
1742629--1742672	22	2.0	22	86	0	61	56	9	6	27	1.55
1742793--1742831	20	2.0	20	85	10	53	46	0	0	53	1.00
1742862--1742903	14	2.9	14	83	13	50	40	2	2	54	1.26
1742976--1743018	17	2.5	18	85	11	63	46	0	0	53	1.00
1742943--1743031	37	2.6	32	81	13	90	48	0	1	50	1.08
1743227--1743673	46	10.4	46	65	20	138	42	2	3	51	1.35
1743302--1743336	14	2.6	14	90	4	54	40	5	0	54	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1743453--1743490	16	2.4	16	86	8	51	42	0	0	57	0.98
1743218--1743719	168	3.0	169	97	0	952	42	2	4	50	1.35
1743591--1743668	21	3.5	21	73	13	57	42	1	2	53	1.22
1743730--1743777	15	2.9	17	72	12	55	52	2	2	43	1.24
1743871--1743921	14	3.6	14	80	12	59	49	0	3	47	1.20
1744419--1744447	11	2.5	12	94	5	51	17	6	17	58	1.59
1745558--1745749	38	5.1	38	90	0	285	27	30	14	27	1.95
1745536--1745646	38	2.6	45	73	19	137	27	36	15	21	1.93
1745558--1745742	76	2.4	76	94	0	316	27	30	14	28	1.95
1752946--1753074	52	2.5	52	93	2	215	30	17	16	36	1.91
1752954--1753094	52	2.7	51	89	4	203	30	17	17	34	1.94
1753083--1753107	13	1.9	13	100	0	50	36	16	16	32	1.90
1753173--1753197	13	1.9	13	100	0	50	32	16	16	36	1.90
1753847--1754050	38	5.4	38	90	0	300	25	30	14	28	1.95
1757500--1757540	8	4.7	9	90	9	59	41	0	2	56	1.13
1758739--1758796	20	3.0	20	75	12	66	50	0	0	50	1.00
1760431--1760468	14	2.9	13	85	11	51	50	0	0	50	1.00
1760435--1760468	14	2.5	14	90	4	52	52	0	0	47	1.00
1763332--1763359	2	14.0	2	100	0	56	50	0	0	50	1.00
1764227--1764251	2	12.5	2	100	0	50	52	0	0	48	1.00
1769494--1769518	12	2.1	12	100	0	50	16	32	28	24	1.96
1769527--1769572	12	3.6	12	78	16	56	45	4	10	39	1.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1769528--1769584	27	2.1	27	86	0	78	42	5	17	35	1.72
1771610--1771675	30	2.2	30	82	15	75	59	3	0	37	1.13
1773848--1773890	14	3.1	13	81	15	50	39	0	2	58	1.11
1775633--1775675	2	22.5	2	90	9	72	48	0	0	51	1.00
1778584--1778623	20	2.0	20	85	0	53	10	10	2	77	1.08
1779797--1779828	2	16.0	2	100	0	64	50	0	0	50	1.00
1780031--1780058	2	14.0	2	100	0	56	50	0	0	50	1.00
1780955--1780979	2	12.5	2	100	0	50	48	0	0	52	1.00
1781770--1781803	13	2.5	14	90	4	52	58	0	0	41	0.98
1791184--1791212	14	2.1	14	100	0	58	37	6	34	20	1.80
1796337--1796368	13	2.5	13	94	0	55	62	3	0	34	1.11
1796337--1796379	13	3.3	13	87	6	52	65	2	0	32	1.06
1797608--1797663	22	2.5	23	79	5	69	48	0	0	51	1.00
1797822--1797865	22	2.0	22	91	8	72	40	0	0	59	0.98
1799392--1799429	12	2.9	13	84	11	51	28	2	5	63	1.30
1801497--1801529	16	2.0	17	88	5	50	15	3	9	72	1.21
1807653--1807687	10	3.5	10	96	0	61	57	8	25	8	1.57
1808621--1808696	27	2.8	27	83	0	80	26	7	17	48	1.74
1811361--1811440	29	2.7	29	82	9	81	63	1	0	35	1.02
1811402--1811452	15	3.4	14	75	21	50	60	0	0	39	0.97
1811411--1811516	18	6.2	16	73	16	63	59	0	0	40	0.97
1811375--1811516	30	4.9	29	75	14	100	61	0	0	38	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1811376--1811495	14	7.8	14	68	26	57	60	0	0	39	0.97
1811824--1811969	76	1.9	76	100	0	292	23	26	14	35	1.93
1812654--1812710	29	2.0	29	96	0	105	26	31	17	24	1.97
1813416--1813480	34	2.0	33	88	8	98	52	0	0	47	1.00
1813440--1813500	29	2.1	29	81	0	68	50	3	3	42	1.34
1813751--1813798	16	3.0	16	87	0	69	54	2	4	39	1.32
1816111--1816173	21	3.0	22	79	11	69	46	0	0	53	1.00
1816312--1816375	13	5.1	12	73	19	51	53	0	0	46	1.00
1816312--1816374	27	2.3	26	81	5	72	52	0	0	47	1.00
1816501--1816554	18	2.9	17	82	15	63	66	7	1	24	1.27
1816527--1816596	31	2.2	31	80	9	79	64	2	0	32	1.08
1819744--1819776	2	16.5	2	100	0	66	51	0	48	0	1.00
1821231--1821289	22	2.7	21	79	10	57	40	5	0	54	1.23
1821383--1821441	26	2.2	28	84	9	86	49	0	1	49	1.11
1824014--1824069	11	5.2	11	72	12	53	51	1	1	44	1.22
1825950--1825992	21	2.0	22	90	9	70	60	2	0	37	1.10
1831055--1831079	2	12.5	2	100	0	50	48	0	0	52	1.00
1837244--1837320	23	3.3	24	77	17	65	44	0	2	53	1.14
1837558--1837591	2	17.0	2	100	0	68	50	0	0	50	1.00
1843843--1843874	14	2.3	14	100	0	64	53	15	12	18	1.73
1847389--1847424	18	2.1	17	90	10	56	72	5	2	19	1.17
1848358--1848404	2	23.5	2	100	0	94	0	48	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1848422--1848451	2	15.0	2	92	0	51	0	0	46	53	1.00
1854488--1854517	2	15.5	2	93	6	53	50	0	0	50	1.00
1859508--1859559	18	2.7	19	77	20	54	63	0	0	36	0.95
1859674--1859751	33	2.3	33	82	8	86	46	5	1	47	1.33
1860823--1860865	21	2.1	21	86	4	61	41	0	0	58	0.98
1863780--1863812	17	1.9	17	88	11	50	33	18	12	36	1.88
1869888--1869920	17	2.0	17	88	5	50	72	0	0	27	0.85
1870289--1870374	21	4.1	22	79	10	74	62	4	1	31	1.23
1870289--1870356	11	6.4	11	73	10	61	61	5	1	30	1.28
1870244--1870374	10	12.6	10	68	16	54	58	4	2	34	1.31
1872337--1872373	16	2.2	17	90	4	58	48	0	2	48	1.15
1872452--1872492	21	2.0	21	90	4	66	39	0	0	60	0.96
1872460--1872502	21	2.0	21	82	8	52	46	0	0	53	1.00
1872484--1872555	25	2.8	25	77	8	65	38	2	0	58	1.13
1872521--1872596	38	2.0	38	89	0	116	35	1	0	63	1.03
1872832--1872858	4	6.8	4	100	0	54	22	0	0	77	0.76
1872941--1873039	16	6.2	16	72	16	71	45	0	0	54	0.99
1872935--1873021	31	2.7	32	80	16	92	45	0	0	54	1.00
1872971--1873053	42	2.0	43	83	7	107	40	0	0	59	0.98
1873013--1873080	20	3.5	19	73	13	57	42	0	0	57	0.98
1877177--1877359	21	8.7	22	73	15	113	56	6	2	34	1.38
1877190--1877325	64	2.1	63	83	1	173	58	5	2	33	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1877190--1877359	10	16.2	11	68	21	80	56	5	2	34	1.39
1877248--1877359	42	2.7	43	82	14	130	53	6	1	38	1.37
1880310--1880345	16	2.2	17	90	5	56	50	0	0	50	1.00
1880433--1880487	18	3.2	18	75	12	62	45	0	0	54	0.99
1880867--1880922	13	4.1	13	70	20	51	44	0	1	53	1.11
1880866--1880955	26	3.4	26	75	18	89	41	0	1	57	1.06
1880883--1880970	18	4.9	18	70	20	60	38	0	1	60	1.04
1880933--1880982	13	3.6	13	80	15	55	34	0	0	66	0.92
1882038--1882215	6	31.0	6	69	20	53	56	0	0	42	1.03
1882079--1882215	17	7.9	17	64	24	63	56	0	0	43	0.99

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