genome.fa.s220.2.7.7.80.10.50.1000.7.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: Scaffold220
Parameters: 2 7 7 80 10 50 1000
Length:  3999181

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   

This is table  7  of  19  ( 2201 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)
1529366--1529408	15	2.7	16	85	7	61	55	0	0	44	0.99
1529366--1529409	16	2.8	15	80	10	52	56	0	0	43	0.99
1529753--1529820	17	3.8	17	74	20	50	30	0	0	69	0.89
1529741--1529804	33	2.0	30	82	8	74	35	0	0	64	0.94
1529740--1529830	27	3.2	29	78	10	91	35	0	0	64	0.94
1529740--1529831	28	3.3	27	74	15	80	34	0	0	65	0.93
1535162--1535198	2	18.5	2	100	0	74	48	0	0	51	1.00
1537559--1537618	21	2.8	21	75	14	59	46	1	1	50	1.21
1538451--1538490	2	20.0	2	100	0	80	50	0	0	50	1.00
1538988--1539034	20	2.5	20	86	6	62	53	0	0	46	1.00
1543255--1543304	24	2.1	24	100	0	100	42	12	12	34	1.79
1546822--1546859	18	2.1	18	85	9	51	55	0	0	44	0.99
1554469--1554520	2	25.5	2	84	3	68	46	1	1	50	1.23
1554475--1554533	27	2.2	27	96	0	109	44	5	3	47	1.42
1554783--1554824	2	21.0	2	95	0	75	47	0	2	50	1.14
1556056--1556145	37	2.3	42	74	18	102	58	0	2	38	1.10
1563108--1563144	2	18.5	2	88	0	56	51	0	2	45	1.15
1563347--1563376	2	15.0	2	100	0	60	0	50	0	50	1.00
1564314--1564348	16	2.2	16	100	0	70	51	11	0	37	1.38
1564313--1564352	20	2.0	20	95	0	71	50	12	0	37	1.41
1564432--1564470	2	19.5	2	89	0	60	43	2	2	51	1.29
1565447--1565476	13	2.2	14	94	5	53	46	6	6	40	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1565692--1565745	17	3.2	17	80	17	51	37	0	1	61	1.07
1566435--1566482	13	3.5	13	78	15	53	45	4	2	47	1.33
1567153--1567404	34	7.5	34	86	4	332	40	26	7	25	1.82
1567153--1567404	68	3.7	68	88	1	373	40	26	7	25	1.82
1571819--1572067	34	7.4	34	87	2	333	40	26	7	25	1.82
1571819--1572067	67	3.7	68	87	2	360	40	26	7	25	1.82
1573953--1573982	9	3.4	9	90	9	53	36	0	0	63	0.95
1574479--1574508	2	15.0	2	100	0	60	50	0	0	50	1.00
1576095--1576125	4	7.8	4	92	0	53	48	22	3	25	1.66
1577141--1577195	27	2.0	27	89	0	83	34	10	20	34	1.87
1581335--1581362	4	7.0	4	100	0	56	25	0	25	50	1.50
1582613--1582644	14	2.3	14	94	0	55	15	9	9	65	1.46
1582779--1582818	2	20.0	2	84	0	53	47	5	2	45	1.38
1582963--1582993	2	15.5	2	100	0	62	51	0	0	48	1.00
1583999--1584049	14	3.9	13	87	10	61	31	3	0	64	1.11
1584014--1584052	14	2.8	14	96	0	69	33	5	0	61	1.18
1585629--1585671	15	2.9	15	80	13	54	46	0	2	51	1.13
1588731--1588764	15	2.3	15	95	5	61	0	8	0	91	0.43
1588737--1588771	16	2.2	16	94	0	61	0	8	2	88	0.61
1588731--1588771	7	5.2	8	80	14	50	0	9	2	87	0.62
1589618--1589650	2	16.0	2	93	6	57	48	0	3	48	1.17
1593242--1593300	18	3.1	19	82	7	66	38	0	0	61	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1593244--1593332	18	5.1	19	69	20	52	40	1	0	58	1.05
1593281--1593351	32	2.2	33	82	12	92	47	1	0	50	1.09
1593275--1593353	16	5.0	16	71	24	53	45	1	0	53	1.08
1593361--1593417	8	6.6	8	75	20	53	29	0	0	70	0.88
1593361--1593417	17	3.3	17	79	15	64	29	0	0	70	0.88
1593371--1593418	11	4.2	12	80	19	59	29	0	0	70	0.87
1593371--1593418	22	2.1	23	92	3	80	29	0	0	70	0.87
1594596--1594632	2	18.5	2	100	0	74	48	0	0	51	1.00
1595614--1595651	13	2.9	13	84	11	51	68	2	0	28	1.03
1596463--1596498	2	18.0	2	100	0	72	0	50	0	50	1.00
1597984--1598031	20	2.3	22	82	13	57	45	2	2	50	1.25
1598142--1598178	16	2.2	17	86	13	51	54	2	2	40	1.29
1600036--1600154	44	2.7	44	86	0	157	31	19	30	19	1.96
1603572--1603596	1	25.0	1	100	0	50	0	100	0	0	0.00
1605466--1605492	2	13.5	2	100	0	54	51	0	0	48	1.00
1611826--1611869	22	2.0	23	90	4	72	52	2	0	45	1.13
1612112--1612160	20	2.4	21	83	12	59	42	0	2	55	1.11
1612141--1612172	15	2.0	17	88	11	50	46	0	0	53	1.00
1612099--1612175	34	2.3	34	82	13	88	45	0	1	53	1.08
1613450--1613669	57	3.9	57	85	4	291	33	22	21	22	1.97
1613848--1613884	19	2.1	19	85	10	51	37	5	8	48	1.56
1616565--1616597	17	1.9	17	93	0	57	42	0	6	51	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1616586--1616658	21	3.5	21	81	9	96	41	1	2	54	1.23
1616506--1616657	11	14.5	11	66	21	51	35	1	3	58	1.28
1616586--1616709	11	11.7	11	70	21	70	41	1	4	51	1.33
1616588--1616723	52	2.6	51	77	10	141	44	1	4	50	1.31
1616797--1616844	14	3.4	14	77	8	53	52	2	0	45	1.12
1621230--1621265	17	2.2	16	90	5	54	44	0	2	52	1.15
1623109--1623194	42	2.0	42	93	0	145	37	11	12	38	1.80
1623826--1623852	2	13.5	2	100	0	54	48	0	0	51	1.00
1624834--1624874	17	2.5	17	84	11	50	63	2	0	34	1.08
1624819--1624908	28	3.3	29	77	14	93	63	1	0	35	1.02
1624851--1624926	39	1.9	39	89	5	118	61	0	0	38	0.96
1626274--1626310	2	18.5	2	100	0	74	51	0	0	48	1.00
1626580--1626610	7	4.4	7	100	0	62	87	0	0	12	0.55
1627156--1627186	13	2.4	13	94	0	53	38	9	0	51	1.35
1627813--1627853	21	2.0	21	95	0	73	31	21	21	24	1.98
1629124--1629158	11	3.4	11	84	15	56	37	0	0	62	0.95
1629121--1629166	20	2.3	20	85	3	67	36	4	0	58	1.18
1630206--1630244	13	3.2	12	82	10	53	64	0	0	35	0.94
1634550--1634610	29	2.1	29	100	0	122	40	19	16	22	1.90
1635238--1635268	10	3.1	10	95	0	53	29	9	3	58	1.46
1639309--1639339	2	15.5	2	93	0	53	51	3	0	45	1.17
1645853--1645882	15	2.0	15	93	0	51	53	10	0	36	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1649167--1649231	33	1.9	35	87	12	100	49	1	1	47	1.20
1649152--1649230	33	2.5	32	76	21	85	49	1	3	45	1.28
1649516--1649592	38	2.0	38	87	7	111	51	0	0	48	1.00
1649731--1649765	2	17.5	2	87	0	52	45	0	5	48	1.26
1653520--1653561	5	8.4	5	89	7	59	40	0	0	59	0.97
1653578--1653626	17	2.9	17	75	9	55	42	0	2	55	1.11
1653565--1653652	34	2.6	32	75	12	86	38	1	1	59	1.13
1653576--1653669	17	5.4	17	69	22	54	38	1	1	59	1.11
1653625--1653670	17	2.6	17	83	13	58	34	2	0	63	1.07
1657322--1657365	2	22.0	2	90	0	70	0	50	2	47	1.13
1661159--1661187	3	9.7	3	100	0	58	68	0	0	31	0.89
1663710--1663774	28	2.3	29	80	15	75	49	0	1	49	1.10
1664603--1664633	2	15.5	2	100	0	62	48	0	0	51	1.00
1665689--1665731	22	2.0	22	85	0	59	11	32	11	44	1.77
1672010--1672062	19	2.6	19	82	8	52	32	0	0	67	0.91
1673063--1673115	22	2.4	22	75	6	54	33	0	0	66	0.92
1673222--1673271	18	2.8	18	68	0	55	56	2	4	38	1.30
1673875--1673906	2	16.0	2	100	0	64	50	0	0	50	1.00
1674895--1674936	22	1.9	22	85	0	57	30	11	2	54	1.49
1674891--1674938	22	2.3	21	79	10	53	33	10	4	52	1.55
1675214--1675252	2	19.5	2	94	0	69	48	2	0	48	1.15
1675613--1675639	2	13.5	2	100	0	54	51	0	48	0	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1676193--1676247	12	4.6	12	80	11	51	60	1	3	34	1.25
1677033--1677088	23	2.5	23	78	18	64	48	0	0	51	1.00
1677079--1677152	30	2.4	30	81	2	76	56	0	0	43	0.99
1677815--1677846	14	2.3	14	94	0	55	43	3	46	6	1.44
1678880--1678904	3	8.3	3	100	0	50	0	32	0	68	0.90
1680270--1680315	23	2.0	23	91	0	74	28	23	10	36	1.89
1682410--1682437	2	14.0	2	100	0	56	50	0	0	50	1.00
1684783--1684807	12	2.1	12	100	0	50	8	52	0	40	1.31
1685267--1685316	23	2.1	24	85	10	68	40	0	4	56	1.18
1691380--1691516	62	2.2	62	87	3	197	29	17	11	40	1.85

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19