genome.fa.s498.2.7.7.80.10.50.1000.15.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: Scaffold498
Parameters: 2 7 7 80 10 50 1000
Length:  1804022

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

This is table  15  of  17  ( 1953 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)
1541985--1542024	20	2.0	20	100	0	80	35	25	15	25	1.94
1544831--1544865	2	17.5	2	93	0	61	48	2	0	48	1.16
1549206--1549243	2	19.0	2	94	0	67	47	0	2	50	1.15
1550217--1550278	16	3.6	17	76	6	54	56	3	0	40	1.15
1551264--1551301	16	2.3	17	90	4	60	57	0	0	42	0.98
1551861--1551911	17	2.9	18	82	11	61	60	1	0	37	1.08
1554597--1554631	9	3.8	9	85	7	52	28	0	0	71	0.86
1558716--1558797	37	2.2	38	80	10	98	51	3	2	42	1.32
1559077--1559117	13	3.0	14	78	7	57	53	0	0	46	1.00
1559057--1559123	27	2.4	27	82	7	80	50	1	0	47	1.10
1560213--1560263	18	2.8	19	79	8	61	66	0	1	31	1.03
1561165--1561202	2	19.0	2	94	0	67	47	0	2	50	1.15
1561927--1562025	36	2.8	36	76	11	107	49	0	0	50	1.00
1562208--1562246	11	3.6	11	86	6	53	53	0	0	46	1.00
1562206--1562246	16	2.6	16	84	0	64	56	0	0	43	0.99
1562483--1562523	3	13.7	3	100	0	82	68	0	0	31	0.90
1562827--1562874	19	2.5	20	83	12	66	35	0	0	64	0.94
1563414--1563476	13	4.5	13	75	19	56	38	0	0	61	0.96
1563410--1563499	25	3.5	26	77	8	78	42	0	0	57	0.98
1563936--1563974	18	2.2	18	86	9	53	46	0	2	51	1.14
1564817--1564885	32	2.1	35	84	13	92	57	0	1	40	1.07
1564839--1564890	27	2.0	27	88	11	81	53	0	0	46	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1564849--1564906	27	2.1	27	81	12	66	58	0	0	41	0.98
1566163--1566203	20	2.0	20	95	0	73	34	7	12	46	1.69
1567444--1567492	23	2.1	24	92	3	82	36	4	2	57	1.30
1567518--1567567	21	2.4	21	93	3	84	24	12	32	32	1.91
1568182--1568212	11	2.8	11	95	0	53	58	0	3	38	1.15
1568192--1568242	17	3.1	16	81	13	59	62	0	0	37	0.95
1568225--1568295	14	5.4	14	68	31	50	52	0	0	47	1.00
1568182--1568276	28	3.3	29	75	18	76	55	0	1	43	1.06
1568233--1568295	18	3.6	19	70	27	59	50	0	0	49	1.00
1568223--1568303	32	2.5	32	81	4	99	50	0	0	49	1.00
1568816--1568853	17	2.2	17	90	0	58	52	13	10	23	1.71
1570368--1570439	18	3.7	19	75	7	74	44	1	2	51	1.24
1570946--1571024	30	2.7	30	84	3	99	54	0	2	43	1.14
1571014--1571055	16	2.8	15	86	13	52	42	0	2	54	1.13
1576364--1576392	2	14.5	2	100	0	58	51	0	0	48	1.00
1576392--1576426	2	17.5	2	100	0	70	51	0	48	0	1.00
1580943--1580975	2	16.5	2	93	0	57	51	3	0	45	1.16
1581511--1581557	15	3.2	15	82	14	62	61	0	2	36	1.08
1581544--1581581	11	3.2	12	82	17	53	50	0	0	50	1.00
1581534--1581599	24	3.0	22	79	14	75	53	0	0	46	1.00
1581530--1581662	61	2.1	64	79	15	145	53	0	0	45	1.05
1581975--1582025	22	2.3	23	80	19	63	52	0	0	47	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1585180--1585204	3	8.3	3	100	0	50	68	0	0	32	0.90
1585846--1585968	48	2.6	48	77	10	128	35	2	5	56	1.36
1585856--1585969	16	7.0	17	77	9	80	35	3	5	55	1.40
1588113--1588164	26	2.0	27	88	3	79	51	1	1	44	1.23
1588185--1588227	19	2.3	18	88	4	59	30	2	0	67	1.03
1588185--1588247	12	5.2	12	74	12	58	31	3	0	65	1.09
1592623--1592679	14	3.6	15	76	23	55	28	5	1	64	1.25
1592629--1592689	16	4.3	14	74	22	56	26	4	1	67	1.20
1592698--1592740	15	2.8	15	83	13	52	46	0	2	51	1.13
1593000--1593032	2	16.5	2	100	0	66	51	0	0	48	1.00
1593218--1593256	17	2.5	15	88	12	60	53	0	0	46	1.00
1593218--1593255	16	2.4	16	91	8	60	55	0	0	44	0.99
1593635--1593690	27	2.0	28	83	10	71	51	0	0	48	1.00
1594094--1594154	20	2.8	22	82	12	81	42	0	0	57	0.98
1594094--1594167	20	3.6	21	80	12	66	44	0	0	55	0.99
1596506--1596556	20	2.5	20	90	0	75	35	19	11	33	1.88
1596588--1596614	13	2.1	13	100	0	54	40	14	14	29	1.86
1599157--1599191	13	2.7	13	86	0	52	37	11	14	37	1.82
1603442--1603466	13	1.9	13	100	0	50	36	16	16	32	1.90
1603484--1603637	20	7.7	19	85	8	200	27	16	13	42	1.86
1603484--1603637	40	3.8	40	96	0	281	27	16	13	42	1.86
1605919--1606097	51	3.5	51	84	2	209	29	25	10	34	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1606080--1606255	76	2.3	79	81	9	211	27	23	15	32	1.96
1606189--1606302	51	2.2	51	84	0	147	30	20	12	36	1.89
1606239--1606413	79	2.2	78	87	5	246	26	24	14	34	1.94
1605982--1606413	206	2.1	207	81	8	504	28	24	13	34	1.93
1606122--1606382	130	2.0	125	83	6	328	27	23	13	35	1.92
1606258--1606413	78	2.0	79	89	3	244	26	23	13	35	1.92
1608131--1608191	13	5.2	13	74	22	71	37	18	13	31	1.88
1608118--1608209	33	2.8	33	96	0	166	36	20	11	30	1.89
1608144--1608209	20	3.7	20	73	26	83	36	21	12	30	1.90
1615072--1615111	16	2.5	16	88	8	55	62	2	7	27	1.35
1615787--1615877	8	10.1	9	68	23	50	35	1	2	61	1.15
1615787--1615879	27	3.5	24	75	19	71	35	1	2	61	1.15
1615814--1615887	5	14.4	5	71	20	55	33	1	1	63	1.11
1615784--1615887	32	3.3	32	72	20	85	35	0	1	61	1.14
1615817--1615889	11	6.7	11	79	13	80	34	1	1	63	1.12
1616257--1616288	2	17.0	2	87	12	50	50	0	0	50	1.00
1616510--1616558	25	2.0	25	84	8	64	51	0	2	46	1.12
1619266--1619303	15	2.5	15	87	12	51	42	0	0	57	0.98
1623908--1623979	26	2.7	26	82	2	90	31	4	15	48	1.64
1624064--1624142	39	2.1	38	90	2	122	16	25	3	54	1.59
1625652--1625703	15	3.6	14	80	19	63	36	0	0	63	0.95
1627880--1627961	41	2.0	41	95	0	146	36	0	9	53	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1627941--1628042	6	17.3	6	71	14	61	37	0	1	60	1.08
1627941--1628002	11	5.5	11	74	16	56	32	0	3	64	1.09
1627940--1628004	29	2.2	30	81	8	80	35	0	3	61	1.12
1628166--1628200	18	1.9	18	88	0	52	51	0	2	45	1.16
1628896--1628932	12	3.2	12	81	11	51	43	0	0	56	0.99
1628900--1628957	22	2.8	22	85	12	70	44	0	0	55	0.99
1628932--1628982	13	4.0	12	79	20	59	50	0	0	49	1.00
1630420--1630461	21	2.0	21	86	9	59	42	0	0	57	0.99
1631523--1631602	26	3.1	27	79	12	80	43	0	0	56	0.99
1631562--1631603	16	2.5	17	77	14	52	45	0	0	54	0.99
1635012--1635052	5	7.8	5	84	10	55	58	0	4	36	1.20
1635015--1635047	17	1.9	17	93	0	57	57	0	6	36	1.23
1635082--1635146	20	3.2	21	75	14	57	43	0	0	56	0.99
1635128--1635206	30	2.6	31	75	11	83	49	0	0	50	1.00
1635759--1635797	12	3.0	12	82	17	51	43	0	7	48	1.31
1635754--1635800	14	3.4	14	80	16	53	40	0	8	51	1.33
1636911--1636958	16	2.8	17	75	12	53	45	2	2	50	1.25
1636899--1636958	17	3.5	17	80	6	50	40	5	1	53	1.33
1637570--1637619	11	4.7	11	79	18	52	46	2	0	52	1.12
1638052--1638127	13	5.8	13	77	7	73	61	1	0	36	1.04
1638052--1638125	28	2.8	26	73	18	62	60	1	0	37	1.05
1638067--1638137	35	2.0	36	83	8	92	60	2	0	36	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1638110--1638166	24	2.3	26	82	17	77	52	7	0	40	1.28
1638346--1638392	15	3.2	15	79	14	53	31	0	0	68	0.90
1639721--1639772	16	3.1	17	83	8	61	44	1	1	51	1.23
1640272--1640320	24	2.0	24	84	0	62	24	0	2	73	0.94
1640279--1640329	24	2.1	24	81	0	57	25	1	1	70	1.08
1640349--1640379	8	3.9	8	100	0	62	22	0	0	77	0.77
1642267--1642318	7	6.9	7	75	16	50	57	0	0	42	0.98
1642495--1642562	4	16.8	4	77	18	54	70	0	26	2	1.01
1642502--1642562	19	3.0	19	81	11	68	70	0	26	3	1.02
1642508--1642562	25	2.2	24	87	9	76	72	0	23	3	1.00

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