genome.fa.s40.2.7.7.80.10.50.1000.12.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: Scaffold40
Parameters: 2 7 7 80 10 50 1000
Length:  3440810

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   

This is table  12  of  24  ( 2833 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)
1646404--1646469	24	2.7	25	86	6	75	43	0	1	54	1.09
1646413--1646469	24	2.3	24	90	3	87	43	0	1	54	1.10
1647615--1647641	12	2.2	12	100	0	54	66	0	7	25	1.17
1648192--1648245	25	2.2	24	83	9	65	51	1	0	46	1.11
1648809--1648848	19	2.2	19	86	4	55	50	2	2	45	1.28
1649712--1649746	16	2.2	16	89	0	52	17	17	22	42	1.88
1650131--1650179	14	3.5	14	78	10	64	34	0	0	65	0.93
1650178--1650241	32	2.0	32	90	3	103	57	0	9	32	1.30
1650693--1650723	14	2.2	14	94	0	53	38	0	6	54	1.26
1651986--1652028	3	14.3	3	100	0	86	32	0	0	67	0.91
1652343--1652398	17	3.5	15	79	16	60	37	0	0	62	0.95
1652339--1652394	15	3.5	15	76	16	51	37	0	0	62	0.95
1652339--1652398	31	1.9	32	86	10	88	38	0	0	61	0.96
1652589--1652626	19	2.1	18	85	14	51	36	0	0	63	0.95
1653037--1653064	2	14.0	2	100	0	56	50	0	0	50	1.00
1653219--1653253	2	17.5	2	100	0	70	48	0	0	51	1.00
1654958--1655001	18	2.4	18	85	14	63	38	0	0	61	0.96
1655668--1655705	11	3.6	11	79	13	53	57	0	7	34	1.28
1655659--1655707	20	2.5	20	96	0	89	59	0	6	34	1.22
1660958--1661031	32	2.2	34	88	4	107	37	0	2	59	1.12
1660973--1661020	25	2.0	23	84	8	60	43	0	0	56	0.99
1661194--1661228	17	2.1	17	88	0	52	45	11	0	42	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1664290--1664351	31	2.0	31	87	3	90	35	0	1	62	1.05
1664290--1664351	15	4.1	16	74	21	62	35	0	1	62	1.05
1664975--1665022	2	24.0	2	100	0	96	50	0	0	50	1.00
1665316--1665399	28	3.0	28	91	0	141	21	10	17	50	1.77
1669891--1669945	28	2.0	28	100	0	110	18	10	21	49	1.78
1669893--1669981	28	3.2	28	84	10	103	21	5	21	51	1.68
1669927--1669981	26	2.0	28	86	6	78	23	3	21	50	1.64
1669897--1669991	28	3.7	24	77	13	66	24	6	21	48	1.73
1671303--1671363	32	1.9	32	86	6	88	44	0	27	27	1.55
1671414--1671463	2	25.0	2	100	0	100	50	0	0	50	1.00
1672280--1672313	16	2.1	16	89	10	52	41	0	2	55	1.15
1674109--1674133	13	1.9	13	100	0	50	8	4	32	56	1.47
1679033--1679067	15	2.3	15	86	13	54	31	0	0	68	0.90
1679627--1679659	13	2.6	13	90	4	50	39	0	0	60	0.97
1679902--1679949	2	24.0	2	82	0	60	47	6	2	43	1.40
1679895--1679933	10	3.9	10	93	0	51	51	5	0	43	1.24
1680475--1680518	21	2.1	21	86	0	61	70	2	2	25	1.10
1680603--1680651	20	2.6	19	84	9	64	32	0	2	65	1.04
1680635--1680675	21	2.0	21	90	9	66	46	0	0	53	1.00
1682645--1682676	10	3.4	10	83	16	50	53	0	0	46	1.00
1684995--1685055	2	30.5	2	96	0	113	47	0	1	50	1.10
1687097--1687122	7	3.7	7	100	0	52	57	15	15	11	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1688496--1688547	26	2.0	27	85	11	72	53	3	9	32	1.51
1688450--1688614	86	1.9	86	92	4	280	50	1	13	33	1.52
1689179--1689203	12	2.1	12	100	0	50	32	24	16	28	1.96
1689391--1689428	16	2.4	17	86	13	62	42	2	0	55	1.14
1689539--1689596	17	3.2	18	72	16	57	37	5	0	56	1.21
1689619--1689657	19	1.9	19	85	10	51	48	12	0	38	1.42
1689656--1689695	20	2.0	20	90	9	64	65	2	0	32	1.06
1690065--1690090	2	13.0	2	100	0	52	50	0	0	50	1.00
1691641--1691666	6	4.3	6	100	0	52	34	0	50	15	1.45
1692551--1692614	31	2.1	31	93	0	110	56	10	9	23	1.63
1693416--1693463	13	3.6	13	80	8	53	64	0	0	35	0.94
1694244--1694345	51	2.0	51	86	0	141	44	13	12	29	1.81
1694495--1694540	15	3.3	14	76	17	51	39	0	2	58	1.10
1695298--1695339	22	1.9	22	85	9	59	40	0	0	59	0.97
1695431--1695483	27	2.0	26	81	3	61	62	11	1	24	1.39
1701934--1701960	3	9.0	3	100	0	54	66	0	0	33	0.92
1704632--1704660	5	5.8	5	100	0	58	0	17	0	82	0.66
1704905--1704956	27	2.0	25	85	7	68	55	1	0	42	1.10
1705966--1706015	25	2.0	25	92	7	84	48	0	2	50	1.12
1706360--1706411	9	5.8	9	76	0	50	51	3	0	44	1.19
1706360--1706414	18	3.1	18	72	0	56	52	3	0	43	1.18
1706471--1706513	23	2.0	22	82	17	54	39	4	0	55	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1706840--1706905	20	3.2	21	71	14	57	40	1	0	57	1.08
1706853--1706913	11	5.5	11	75	11	52	40	1	0	57	1.08
1707773--1707806	15	2.2	16	94	5	61	29	0	5	64	1.17
1707878--1707945	31	2.4	28	85	9	84	52	0	1	45	1.09
1708019--1708080	23	2.7	22	74	16	56	58	1	0	40	1.08
1707915--1708292	116	3.4	109	82	13	449	52	1	2	43	1.23
1707909--1708098	41	4.9	38	69	20	117	53	1	1	44	1.14
1708176--1708246	31	2.3	31	83	9	83	53	0	2	43	1.15
1708581--1708925	122	2.9	119	86	9	460	42	2	2	53	1.24
1708617--1708925	123	2.7	115	85	10	391	43	1	2	52	1.24
1709380--1710171	177	4.5	178	80	10	813	41	7	16	34	1.75
1709380--1710171	92	8.9	88	81	7	777	41	7	16	34	1.75
1712719--1712786	22	3.1	21	78	14	57	58	0	1	39	1.07
1717664--1717699	18	2.0	19	89	10	58	25	0	13	61	1.33
1719694--1719736	3	13.7	3	90	9	68	65	0	0	34	0.93
1719694--1719736	22	2.0	22	95	0	77	65	0	0	34	0.93
1719797--1719832	12	2.8	13	87	4	56	38	2	0	58	1.13
1719758--1719890	69	1.9	71	81	6	155	46	3	3	47	1.33
1719915--1719954	20	2.0	21	90	9	66	55	0	0	45	0.99
1720076--1720109	18	1.9	18	88	5	52	64	0	2	32	1.08
1720114--1720151	20	2.0	19	90	10	60	31	2	5	60	1.33
1720421--1720450	5	5.8	5	92	7	51	56	20	0	23	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1720421--1720450	11	2.9	10	90	9	51	56	20	0	23	1.42
1724177--1724212	2	18.0	2	100	0	72	50	0	0	50	1.00
1729333--1729375	18	2.3	18	88	4	59	41	2	0	55	1.12
1729617--1729643	5	5.4	5	100	0	54	81	0	0	18	0.69
1730155--1730194	20	2.1	19	85	4	53	42	0	0	57	0.98
1730289--1730316	14	2.0	14	100	0	56	28	0	0	71	0.86
1730818--1730848	14	2.2	14	94	0	53	83	0	16	0	0.64
1730814--1730851	18	2.1	18	90	0	58	84	0	15	0	0.63
1732608--1732651	20	2.2	20	84	12	54	45	2	0	52	1.13
1733740--1733822	18	4.6	18	71	20	66	42	1	0	56	1.07
1735260--1735344	42	2.0	42	93	0	143	21	12	20	45	1.84
1736240--1736617	197	1.9	197	92	0	639	23	10	18	47	1.79
1737012--1737052	13	3.2	13	80	16	50	24	0	12	63	1.28
1739191--1739259	29	2.3	30	85	2	86	60	1	1	36	1.14
1739207--1739260	13	3.9	13	75	13	54	62	0	1	35	1.06
1739597--1739646	22	2.2	23	82	3	57	44	6	0	50	1.26
1742096--1742162	25	2.6	25	80	2	62	61	1	0	37	1.05
1742184--1742253	23	3.0	24	82	12	76	38	5	1	54	1.33
1743213--1743256	21	2.1	21	87	8	63	65	2	0	31	1.05
1743211--1743264	21	2.7	19	80	11	56	66	3	0	29	1.09
1743429--1743464	16	2.3	15	90	4	54	44	2	2	50	1.31
1743881--1743942	24	2.6	24	77	15	74	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)
1743897--1743973	20	3.9	20	68	22	56	58	1	0	40	1.06
1743894--1743973	38	2.2	37	80	12	94	58	1	0	40	1.06
1745431--1745470	15	2.9	14	85	10	55	37	0	2	60	1.11
1746786--1746842	17	3.4	17	80	11	64	45	1	0	52	1.11
1747015--1747048	12	2.8	12	90	4	50	70	0	2	26	1.01
1747057--1747126	18	3.9	17	76	14	52	61	4	0	34	1.16
1747434--1747464	14	2.2	14	100	0	62	58	22	12	6	1.58
1749001--1749027	4	6.8	4	100	0	54	77	0	0	22	0.76
1753576--1753635	28	2.1	28	81	6	68	43	0	0	56	0.99
1753591--1753635	15	3.1	15	78	12	58	40	0	0	60	0.97

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