genome.fa.s8.2.7.7.80.10.50.1000.12.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: 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  12  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)
1585581--1585637	18	3.1	18	72	22	55	61	1	5	31	1.28
1586905--1587004	19	5.1	19	73	17	73	33	1	0	66	0.99
1586914--1587022	19	6.0	17	70	22	62	33	1	0	64	1.05
1586908--1587022	10	12.0	10	67	22	52	33	1	0	64	1.04
1587075--1587101	4	6.8	4	100	0	54	77	0	0	22	0.76
1587507--1587546	21	1.9	21	89	0	62	52	0	7	40	1.30
1587481--1587517	3	12.3	3	100	0	74	67	0	0	32	0.91
1587602--1587633	5	6.4	5	100	0	64	18	0	0	81	0.70
1588845--1588885	21	2.1	21	86	13	61	60	0	0	39	0.96
1588884--1588927	19	2.3	18	85	11	61	45	0	0	54	0.99
1588891--1588946	27	1.9	30	82	13	73	53	0	0	46	1.00
1588884--1588942	20	3.0	20	81	16	63	49	0	0	50	1.00
1588927--1588970	21	2.0	22	83	16	56	70	0	0	29	0.88
1588960--1588993	13	2.4	15	90	9	54	79	0	5	14	0.91
1589308--1589369	31	2.0	30	84	9	79	43	0	0	56	0.99
1595498--1595529	2	16.0	2	100	0	64	50	50	0	0	1.00
1595498--1595543	12	3.8	12	91	0	56	54	41	0	4	1.20
1598416--1598440	8	3.1	8	100	0	50	88	0	0	12	0.53
1599139--1599171	7	4.9	7	88	7	50	0	12	3	84	0.72
1599139--1599171	13	2.4	14	90	5	50	0	12	3	84	0.72
1599443--1599514	35	2.1	35	100	0	144	47	8	22	22	1.77
1599631--1599820	47	4.0	47	99	0	371	48	23	6	21	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1604611--1604814	106	1.9	107	96	1	383	29	14	10	45	1.79
1605888--1605925	2	19.0	2	100	0	76	50	0	0	50	1.00
1618212--1618261	27	2.0	26	81	14	61	50	2	2	46	1.24
1618818--1618868	23	2.2	24	82	10	61	62	1	3	31	1.24
1618877--1618951	14	4.8	16	72	23	61	53	0	4	42	1.19
1618877--1618950	30	2.3	32	88	6	107	52	0	4	43	1.20
1619481--1619527	19	2.4	21	80	16	57	57	4	0	38	1.18
1619574--1619632	29	2.1	28	81	9	66	57	3	5	33	1.37
1620048--1620072	13	1.9	13	100	0	50	56	0	0	44	0.99
1620056--1620090	18	1.9	18	94	0	61	45	0	0	54	0.99
1620058--1620102	18	2.5	17	82	7	54	48	0	0	51	1.00
1620802--1620848	6	7.8	6	81	9	60	63	0	4	31	1.13
1621912--1622037	41	3.0	42	71	13	109	57	3	1	36	1.27
1622009--1622061	18	2.8	19	77	11	56	58	3	1	35	1.27
1622009--1622086	17	4.8	17	71	24	53	60	3	1	34	1.23
1622835--1622863	3	9.7	3	100	0	58	65	0	0	34	0.93
1622945--1622981	19	1.9	19	89	10	58	45	5	5	43	1.49
1623162--1623194	2	17.0	2	93	6	59	51	0	0	48	1.00
1626182--1626223	16	2.5	17	88	3	59	38	0	2	59	1.10
1627079--1627138	19	3.5	17	74	12	52	35	3	6	55	1.43
1628468--1628533	21	3.2	21	77	10	55	66	0	1	31	1.01
1628651--1628722	15	4.4	16	75	17	69	55	0	0	44	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1628663--1628728	35	1.9	33	90	6	105	54	0	0	45	0.99
1633189--1633238	23	2.2	23	82	7	57	56	0	4	40	1.18
1633202--1633245	22	2.0	22	82	8	54	59	0	2	38	1.10
1633211--1633279	18	4.0	17	77	5	68	53	0	2	43	1.15
1633255--1633310	9	6.0	9	77	20	53	41	0	1	57	1.09
1633258--1633318	17	3.3	17	72	22	52	37	0	1	60	1.07
1636073--1636130	28	2.1	28	93	0	98	24	20	18	36	1.95
1636606--1636636	2	15.5	2	100	0	62	48	0	0	51	1.00
1637446--1637482	2	18.5	2	88	0	56	48	5	0	45	1.25
1640956--1641028	34	2.2	34	82	2	85	41	17	10	30	1.84
1645052--1645090	20	1.9	19	85	10	51	20	0	5	74	1.01
1645301--1645332	16	2.0	16	93	0	55	46	0	3	50	1.17
1645436--1645461	8	3.2	8	100	0	52	65	0	0	34	0.93
1645871--1645920	22	2.3	22	82	6	66	50	0	0	50	1.00
1645947--1645971	12	2.1	12	100	0	50	60	0	0	40	0.97
1646422--1646484	26	2.4	25	73	19	58	42	1	1	53	1.19
1647829--1647857	2	14.5	2	100	0	58	51	0	0	48	1.00
1648780--1648834	2	27.5	2	92	0	92	52	0	0	47	1.00
1648906--1649123	34	6.4	34	85	2	278	25	7	26	40	1.82
1648906--1649123	102	2.1	101	91	1	355	25	7	26	40	1.82
1649430--1649490	19	3.2	19	84	9	79	31	18	13	37	1.88
1653556--1653774	34	6.5	34	85	2	280	25	7	26	40	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1653556--1653774	102	2.2	101	91	1	357	25	7	26	40	1.82
1654339--1654373	11	3.0	12	83	8	54	71	0	0	28	0.86
1654339--1654389	11	4.9	10	79	13	50	68	0	0	31	0.90
1654345--1654389	20	2.3	19	80	3	54	68	0	0	31	0.89
1654830--1655051	114	1.9	118	89	5	353	27	13	20	38	1.90
1655380--1655405	3	8.7	3	100	0	52	30	0	0	69	0.89
1659899--1659952	25	2.2	24	83	9	65	35	0	0	64	0.94
1659909--1659962	22	2.5	22	82	8	67	35	1	0	62	1.06
1661949--1662046	30	3.2	30	76	11	92	44	2	5	47	1.36
1662340--1662412	25	3.0	25	73	18	64	41	1	2	54	1.23
1662419--1662490	30	2.4	30	88	4	101	47	1	6	44	1.38
1661873--1662789	465	2.0	453	87	6	1301	42	5	6	45	1.51
1667047--1667097	18	2.9	18	88	2	68	56	0	0	43	0.99
1667033--1667086	28	2.0	27	82	10	65	53	0	1	44	1.11
1670012--1670064	11	4.9	11	81	4	63	41	0	0	58	0.98
1670207--1670264	26	2.3	26	79	11	66	48	0	0	51	1.00
1670645--1670687	21	2.0	21	100	0	86	48	0	0	51	1.00
1670658--1670701	15	2.9	16	80	13	65	45	0	0	54	0.99
1671176--1671227	20	2.4	21	81	18	63	65	0	0	34	0.93
1674318--1674381	20	2.9	21	77	13	58	29	4	0	65	1.13
1674449--1674477	4	7.5	4	92	7	51	24	0	0	75	0.80
1674474--1674514	8	5.2	8	82	11	50	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1676131--1676169	2	19.5	2	94	0	69	0	51	0	48	1.00
1682742--1682775	2	17.0	2	93	0	59	47	0	2	50	1.16
1684082--1684144	25	2.7	24	76	16	60	68	4	3	23	1.24
1684390--1684444	19	2.7	20	86	10	76	43	0	1	54	1.10
1684368--1684506	57	2.3	59	79	9	140	43	0	2	53	1.18
1684372--1684502	56	2.2	59	80	10	142	45	0	2	51	1.19
1684626--1684675	25	2.0	26	84	11	68	46	2	6	46	1.39
1689662--1689707	2	23.0	2	95	0	83	50	2	0	47	1.13
1690219--1690295	33	2.3	33	78	12	79	53	0	2	44	1.14
1698121--1698200	41	2.0	41	89	0	124	30	20	16	33	1.94
1701198--1701457	126	2.0	131	94	4	467	40	9	10	39	1.72
1701930--1701989	2	32.5	2	80	15	76	46	0	0	53	1.00
1703313--1703352	21	1.9	21	89	0	62	60	12	2	25	1.45
1705174--1705205	15	2.1	15	100	0	64	34	18	40	6	1.76
1705814--1705863	3	16.7	3	100	0	100	32	0	0	68	0.90
1710545--1710608	16	3.9	16	75	20	53	39	0	1	59	1.07
1710558--1710644	33	2.6	33	82	7	88	42	0	1	56	1.07
1713986--1714027	2	21.0	2	100	0	84	50	0	0	50	1.00
1720624--1720666	14	3.1	13	81	15	50	39	0	2	58	1.11
1720612--1720718	57	2.0	52	80	12	117	47	3	0	47	1.26
1720736--1720787	18	3.0	17	86	11	70	51	0	0	48	1.00
1720769--1720812	21	2.0	22	82	4	54	47	4	0	47	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1720932--1720975	23	2.0	23	91	8	74	50	0	4	45	1.22
1720876--1720963	37	2.3	39	80	7	101	46	0	4	48	1.22
1721077--1721111	14	2.6	14	90	4	54	40	5	0	54	1.24
1720984--1721327	170	2.0	171	88	3	507	42	3	4	49	1.39
1722274--1722312	20	2.0	20	89	0	60	35	0	5	58	1.20
1722867--1722894	2	14.0	2	100	0	56	50	0	0	50	1.00
1723877--1724092	34	6.4	34	88	1	292	24	7	27	40	1.83
1723877--1724094	67	3.2	67	88	1	319	24	7	27	40	1.82
1728503--1728720	34	6.5	34	88	1	296	24	7	27	40	1.82
1728503--1728722	67	3.3	67	88	1	323	24	7	27	40	1.82

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