genome.fa.s11.2.7.7.80.10.50.1000.12.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: Scaffold11
Parameters: 2 7 7 80 10 50 1000
Length:  5230303

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   

This is table  12  of  29  ( 3461 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)
1613570--1613620	20	2.7	19	82	17	70	49	0	1	49	1.12
1615678--1615706	2	14.5	2	100	0	58	48	0	0	51	1.00
1617451--1617516	31	2.2	29	82	15	80	53	0	1	45	1.09
1618003--1618067	26	2.3	30	80	15	77	49	0	1	49	1.10
1618552--1618595	19	2.4	19	81	7	56	47	4	4	43	1.44
1621688--1621796	5	21.4	5	68	17	55	59	3	0	36	1.15
1621677--1621727	18	2.5	21	72	21	54	68	1	0	29	1.00
1621815--1621846	2	16.0	2	100	0	64	50	0	0	50	1.00
1623512--1623544	3	11.0	3	100	0	66	33	0	0	66	0.92
1625106--1625142	19	1.9	19	89	10	58	29	5	0	64	1.15
1625180--1625256	29	2.6	29	80	12	86	41	9	1	48	1.43
1625586--1625638	14	4.3	13	77	18	60	71	0	0	28	0.86
1625584--1625647	22	2.8	23	80	17	80	70	0	0	29	0.88
1625586--1625648	10	5.6	10	74	22	54	71	0	0	28	0.86
1627536--1627565	16	1.9	15	93	6	51	0	26	0	73	0.84
1628662--1628689	2	14.0	2	100	0	56	50	0	0	50	1.00
1630609--1630645	7	5.3	7	96	0	65	35	24	13	27	1.93
1633954--1634015	17	3.2	19	78	19	58	67	6	0	25	1.14
1634190--1634232	14	3.1	14	75	0	50	55	0	0	44	0.99
1634515--1634568	21	2.5	23	76	8	60	40	3	1	53	1.29
1634585--1634614	12	2.5	12	94	0	51	43	3	0	53	1.17
1634741--1634785	17	2.6	17	92	0	72	73	2	0	24	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1634741--1634793	17	3.1	17	83	8	63	71	3	0	24	1.02
1635158--1635191	17	2.0	17	88	0	50	58	0	0	41	0.98
1636477--1636514	12	3.2	12	85	3	51	71	0	0	28	0.87
1636544--1636617	18	4.0	20	63	16	52	59	1	0	39	1.06
1636605--1636655	22	2.3	22	83	12	61	66	5	5	21	1.35
1636652--1636701	17	3.0	16	77	8	55	64	0	2	34	1.05
1637299--1637331	17	2.0	17	88	5	50	57	0	0	42	0.98
1637614--1637655	22	2.0	22	90	4	68	54	0	2	42	1.13
1637786--1637848	24	2.5	26	77	15	69	39	4	1	53	1.31
1639136--1639161	2	13.0	2	100	0	52	50	0	0	50	1.00
1644408--1644455	2	24.0	2	86	0	69	45	2	4	47	1.33
1647735--1647767	2	16.5	2	93	0	57	48	0	3	48	1.17
1648402--1648436	12	2.9	12	91	0	52	17	28	20	34	1.95
1650765--1650807	20	2.3	19	84	8	52	55	0	2	41	1.12
1650838--1650876	17	2.2	19	82	17	57	25	0	0	74	0.82
1650864--1650910	21	2.2	21	85	7	60	40	0	2	57	1.11
1653187--1653237	22	2.4	22	83	3	59	56	0	0	43	0.99
1653187--1653228	20	2.0	20	82	13	50	61	0	0	38	0.96
1657304--1657331	2	14.0	2	100	0	56	50	0	0	50	1.00
1658266--1658316	21	2.4	22	83	12	70	43	0	1	54	1.11
1659842--1659876	3	11.7	3	100	0	70	65	0	0	34	0.93
1659969--1660021	23	2.3	23	86	0	79	37	3	3	54	1.36
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1659992--1660160	90	1.9	92	86	2	243	46	2	5	45	1.38
1660395--1660442	24	2.0	25	84	8	64	50	2	0	47	1.12
1660404--1660450	24	2.0	24	87	8	69	51	0	0	48	1.00
1660410--1660449	21	2.0	21	90	5	64	50	0	0	50	1.00
1660817--1660865	3	16.3	3	100	0	98	67	0	0	32	0.91
1661202--1661255	19	2.7	21	80	11	60	57	0	0	42	0.98
1662992--1663072	28	2.9	27	83	3	81	33	2	16	48	1.59
1665561--1665619	21	2.8	22	73	17	61	54	1	0	44	1.10
1665576--1665613	20	1.9	20	84	10	51	47	2	0	50	1.15
1671615--1671643	1	29.0	1	100	0	58	0	0	0	100	0.00
1672248--1672299	26	2.0	26	100	0	104	46	15	11	26	1.80
1673086--1673126	21	2.0	20	85	4	55	48	0	0	51	1.00
1673117--1673162	16	2.9	16	78	12	58	54	0	0	45	0.99
1673097--1673159	28	2.1	29	86	13	85	50	0	0	49	1.00
1674161--1674192	15	2.2	14	94	5	55	59	0	0	40	0.97
1674225--1674265	20	2.0	21	86	13	59	68	0	0	31	0.90
1675169--1675399	122	1.9	120	96	1	426	29	26	12	31	1.93
1682188--1682331	78	1.8	78	92	0	243	32	23	18	25	1.97
1682007--1682514	261	2.0	258	89	3	788	33	22	18	25	1.97
1683809--1683867	28	2.1	28	87	0	82	16	13	30	38	1.88
1684313--1684344	2	16.0	2	100	0	64	50	0	0	50	1.00
1684803--1684836	5	6.4	5	93	6	50	44	17	0	38	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1684983--1685027	23	2.0	23	95	0	81	31	8	8	51	1.64
1685163--1685209	2	24.0	2	86	4	69	55	0	0	44	0.99
1685171--1685208	19	2.0	19	94	0	67	55	0	0	44	0.99
1686697--1686826	52	2.5	53	98	1	253	35	23	13	27	1.92
1686778--1686929	59	2.5	59	80	4	162	39	21	11	26	1.88
1690012--1690059	24	1.9	26	83	8	64	31	0	4	64	1.12
1693269--1693654	194	2.0	194	84	7	509	28	14	13	44	1.83
1708385--1708459	16	4.9	15	76	15	66	42	1	0	56	1.08
1708383--1708459	31	2.5	30	80	14	86	42	1	0	55	1.07
1708418--1708470	17	3.0	18	80	17	58	45	0	0	54	0.99
1708418--1708461	20	2.3	20	85	11	58	47	0	0	52	1.00
1717808--1717964	84	1.9	84	87	0	233	33	14	18	33	1.91
1719699--1719743	3	15.0	3	100	0	90	66	0	0	33	0.92
1730888--1730920	2	16.5	2	100	0	66	51	0	48	0	1.00
1731771--1731815	23	2.0	23	82	8	56	51	0	0	48	1.00
1732703--1732753	22	2.4	22	80	3	59	52	0	1	45	1.12
1733306--1733384	22	3.5	22	67	16	54	53	0	0	46	1.00
1733832--1733877	21	2.3	20	78	10	51	73	0	4	21	1.00
1734665--1734698	17	1.9	18	94	5	61	47	0	0	52	1.00
1734669--1734724	29	1.9	30	89	7	89	44	0	0	55	0.99
1734669--1734724	28	2.0	28	86	10	78	44	0	0	55	0.99
1735251--1735312	16	3.8	17	77	22	55	54	0	0	45	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1735239--1735497	132	1.9	133	93	1	448	50	5	3	40	1.41
1735419--1735477	14	4.0	15	73	10	50	59	0	0	40	0.97
1735453--1735532	40	2.0	40	90	0	124	48	10	3	37	1.55
1737731--1737765	2	18.0	2	94	5	63	51	0	0	48	1.00
1738753--1738791	2	19.5	2	89	0	51	46	5	0	48	1.24
1738948--1738988	2	21.0	2	95	5	75	51	0	0	48	1.00
1742115--1742224	50	2.2	49	79	12	116	46	0	0	53	1.00
1748167--1748235	25	2.8	24	81	12	79	53	1	0	44	1.09
1748166--1748243	6	12.5	6	74	16	61	51	1	0	47	1.09
1748857--1748890	13	2.6	13	85	0	50	52	5	0	41	1.25
1753165--1753192	12	2.3	12	100	0	56	32	0	0	67	0.91
1754189--1754222	15	2.3	15	90	10	52	47	0	0	52	1.00
1757949--1757986	17	2.3	17	86	4	51	57	0	0	42	0.98
1758009--1758042	2	17.5	2	87	6	52	47	0	2	50	1.16
1758287--1758320	3	11.3	3	100	0	68	67	0	0	32	0.91
1758430--1758551	18	6.9	17	69	23	58	40	0	0	59	0.98
1758428--1758538	16	6.9	15	68	16	55	42	0	0	57	0.98
1761976--1762022	24	2.0	24	83	4	60	42	6	10	40	1.65
1762244--1762300	29	2.0	29	89	6	89	61	15	0	22	1.34
1767445--1767513	27	2.6	27	93	4	113	23	13	10	53	1.69
1769881--1770099	34	6.5	33	83	5	267	41	25	7	25	1.82
1769883--1770099	68	3.2	68	84	3	294	41	25	7	25	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1769881--1770099	102	2.2	101	87	1	330	41	25	7	25	1.82
1770787--1770940	77	2.0	76	97	1	290	51	16	11	20	1.74
1770986--1771012	14	1.9	14	100	0	54	62	0	7	29	1.22
1771154--1771188	3	11.7	3	93	0	61	62	0	2	34	1.10
1771660--1771711	5	9.6	5	76	15	50	57	3	0	38	1.17
1771660--1771711	11	4.7	11	83	7	70	57	3	0	38	1.17
1771998--1772044	18	2.8	17	84	9	69	59	0	0	40	0.97
1772240--1772321	42	1.9	43	82	7	105	46	1	0	52	1.08
1772920--1772957	18	2.2	18	86	9	53	34	0	2	63	1.09
1773856--1773885	16	1.9	15	93	6	51	63	3	0	33	1.11

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