genome.fa.s60.2.7.7.80.10.50.1000.11.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: Scaffold60
Parameters: 2 7 7 80 10 50 1000
Length:  3815296

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   

This is table  11  of  21  ( 2419 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)
1530445--1530481	2	19.5	2	89	10	60	51	0	48	0	1.00
1530676--1530708	13	2.6	13	95	4	59	33	0	0	66	0.92
1530801--1530834	17	1.9	17	88	5	50	29	0	0	70	0.87
1531798--1531827	13	2.2	14	94	5	53	76	0	0	23	0.78
1531798--1531828	14	2.2	14	94	0	53	77	0	0	22	0.77
1533494--1533533	19	2.1	19	90	9	64	27	2	0	70	1.01
1534750--1534782	2	16.5	2	100	0	66	48	0	0	51	1.00
1534720--1534844	62	2.0	62	92	3	207	36	7	10	46	1.66
1539200--1539227	4	7.0	4	100	0	56	75	0	25	0	0.81
1539689--1539785	49	1.9	51	85	6	135	53	1	1	44	1.14
1539703--1539764	17	3.8	17	74	22	51	54	0	0	45	0.99
1539689--1539784	50	1.9	49	83	8	122	53	1	1	44	1.14
1555024--1555073	24	2.1	24	84	0	64	56	2	2	40	1.22
1555261--1555317	25	2.2	26	81	9	64	21	0	8	70	1.14
1555568--1555624	25	2.2	26	81	9	64	21	0	8	70	1.14
1555198--1555774	307	1.9	307	97	0	1091	33	5	7	53	1.51
1556084--1556135	18	3.1	18	76	20	58	32	0	0	67	0.91
1556491--1556525	16	2.2	16	90	10	54	54	0	0	45	0.99
1556501--1556549	24	2.0	25	92	4	82	59	0	0	40	0.98
1556516--1556600	31	2.8	31	75	7	84	55	0	1	43	1.07
1556545--1556594	23	2.3	23	86	6	68	52	0	0	48	1.00
1556858--1556905	24	2.2	23	78	14	57	37	0	4	58	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1561866--1561923	22	2.7	21	77	17	64	37	5	0	56	1.21
1563890--1563921	2	16.0	2	93	0	55	46	3	0	50	1.17
1565229--1565277	22	2.3	21	79	10	55	55	0	0	44	0.99
1565376--1565476	49	2.1	49	100	0	202	35	11	29	22	1.90
1567390--1567415	1	26.0	1	100	0	52	0	0	100	0	0.00
1568407--1568831	212	2.0	213	94	0	744	43	16	14	25	1.86
1571537--1571584	23	2.1	24	85	11	66	33	0	2	64	1.05
1571634--1571690	21	2.8	20	74	15	55	63	0	0	36	0.95
1571634--1571689	19	2.8	20	78	13	62	62	0	0	37	0.95
1571643--1571702	29	2.1	27	85	11	77	65	0	1	33	1.03
1577934--1577963	2	15.0	2	100	0	60	50	0	0	50	1.00
1580372--1580406	15	2.3	15	90	0	52	48	0	0	51	1.00
1581636--1581668	16	2.1	17	88	11	52	42	0	0	57	0.98
1597385--1597430	21	2.1	22	88	4	67	45	4	2	47	1.34
1602236--1602326	17	5.5	17	70	16	66	36	0	2	61	1.08
1602266--1602342	33	2.3	34	81	2	84	36	1	1	61	1.13
1608509--1608562	16	3.2	18	70	15	53	55	0	0	44	0.99
1608503--1608565	32	1.9	33	90	9	103	53	0	0	46	1.00
1613494--1613522	2	14.5	2	100	0	58	51	0	48	0	1.00
1614408--1614471	33	1.9	33	84	6	85	46	0	4	48	1.23
1622766--1622791	2	13.0	2	100	0	52	50	0	0	50	1.00
1625630--1625662	2	16.5	2	100	0	66	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1625651--1625691	22	2.0	22	85	9	59	26	12	4	56	1.56
1626459--1626506	19	2.5	19	86	3	60	33	2	4	60	1.27
1626569--1626623	14	3.9	14	77	17	53	40	1	0	58	1.09
1626572--1626612	21	1.9	21	90	5	64	39	2	0	58	1.11
1626576--1626636	25	2.7	21	76	18	59	39	3	1	55	1.26
1626667--1626694	3	9.3	3	100	0	56	35	0	0	64	0.94
1627176--1627218	18	2.5	17	77	7	50	55	0	6	37	1.27
1627227--1627268	20	2.1	20	95	0	75	35	4	14	45	1.66
1627491--1627525	17	2.1	17	89	5	54	54	0	0	45	0.99
1632475--1632513	2	19.5	2	100	0	78	51	0	0	48	1.00
1632775--1632825	14	3.9	13	85	15	54	78	0	21	0	0.75
1632797--1632825	7	4.3	7	95	4	51	75	0	24	0	0.80
1641713--1641747	2	17.5	2	100	0	70	48	0	0	51	1.00
1644936--1644977	15	2.8	16	78	10	52	66	0	0	33	0.92
1655347--1655387	3	13.7	3	100	0	82	65	0	0	34	0.93
1655647--1655696	18	2.8	18	81	9	66	60	2	0	38	1.09
1656415--1656458	3	14.7	3	100	0	88	68	0	0	31	0.90
1657009--1657057	24	2.0	24	84	0	62	44	2	0	53	1.12
1663350--1663449	50	2.0	50	90	0	155	20	25	24	31	1.98
1666632--1666668	2	19.0	2	88	5	58	51	2	0	45	1.15
1667098--1667200	18	6.0	18	69	22	55	44	0	0	54	1.06
1667136--1667197	16	3.8	16	78	19	65	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)
1667169--1667251	22	3.6	22	77	13	87	34	2	0	62	1.08
1667191--1667255	26	2.5	26	78	9	87	33	3	0	63	1.10
1669302--1669349	14	3.5	14	78	13	55	54	2	2	41	1.24
1671408--1671436	2	14.5	2	100	0	58	51	0	0	48	1.00
1680201--1680260	13	4.8	12	76	13	59	50	0	0	50	1.00
1681949--1681987	12	3.1	12	88	7	51	48	0	0	51	1.00
1682383--1682464	28	2.8	30	75	16	82	41	1	0	57	1.06
1682389--1682475	28	3.0	29	77	14	74	41	2	1	55	1.20
1687145--1687181	15	2.3	17	90	9	60	27	0	0	72	0.84
1692607--1692631	13	1.9	13	100	0	50	68	0	0	32	0.90
1693129--1693175	18	2.4	20	86	10	62	36	0	0	63	0.94
1694135--1694170	2	18.0	2	100	0	72	50	0	0	50	1.00
1694719--1694751	17	1.9	17	93	0	57	45	3	6	45	1.43
1699668--1699734	35	1.9	34	90	3	107	25	25	13	35	1.92
1701418--1701451	14	2.3	15	90	5	52	88	5	5	0	0.64
1711459--1711531	25	2.9	26	82	11	89	60	2	0	36	1.11
1711845--1711933	31	2.8	32	74	14	87	52	2	0	44	1.13
1711871--1711914	23	1.9	23	86	9	63	61	2	0	36	1.09
1712180--1712209	15	2.1	14	93	6	51	16	0	0	83	0.65
1712604--1712653	22	2.2	24	82	13	61	48	4	4	44	1.40
1712976--1713006	2	15.5	2	100	0	62	48	0	0	51	1.00
1713703--1713733	14	2.2	14	100	0	62	32	0	0	67	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1714592--1714633	14	2.8	16	79	17	54	50	0	0	50	1.00
1714749--1714813	31	2.0	30	83	16	78	44	0	0	55	0.99
1715202--1715258	24	2.2	27	87	9	84	52	0	0	47	1.00
1715438--1715462	13	1.9	13	100	0	50	76	0	0	24	0.80
1716164--1716188	11	2.3	11	100	0	50	32	0	0	68	0.90
1718166--1718216	21	2.5	21	81	15	70	43	0	3	52	1.19
1721596--1721639	10	4.5	10	78	16	56	72	0	0	27	0.85
1722796--1722894	27	3.5	27	74	17	76	45	1	0	53	1.07
1722817--1722869	20	2.7	19	80	8	52	50	1	0	47	1.12
1722900--1722944	5	9.0	5	85	9	65	37	0	0	62	0.96
1722814--1722925	57	1.9	59	80	12	133	42	0	0	56	1.05
1722900--1722959	15	3.8	16	84	10	70	38	0	1	60	1.07
1722914--1722965	17	3.1	17	78	13	54	42	0	1	55	1.10
1723092--1723121	2	15.0	2	100	0	60	50	0	0	50	1.00
1723425--1723478	22	2.5	21	87	6	72	62	0	1	35	1.06
1724906--1724963	26	2.2	27	84	9	75	53	0	5	41	1.23
1724906--1724983	27	2.9	27	83	9	81	51	0	3	44	1.19
1724953--1724983	15	2.1	15	93	0	53	48	0	0	51	1.00
1725928--1726029	34	3.0	34	75	13	93	40	1	1	55	1.22
1725973--1726039	16	4.2	16	72	22	61	37	1	0	61	1.05
1725984--1726041	9	6.9	9	72	21	54	34	1	0	63	1.04
1726007--1726051	24	1.9	23	86	13	65	31	0	2	66	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1726201--1726238	20	1.9	20	88	0	58	44	0	2	52	1.14
1726262--1726323	23	2.7	23	73	14	65	48	0	1	50	1.10
1726283--1726342	30	2.0	30	83	6	77	46	0	3	50	1.18
1732612--1732653	2	21.0	2	100	0	84	0	50	0	50	1.00
1735360--1735414	21	2.8	19	82	15	67	43	0	1	54	1.10
1739338--1739364	2	13.5	2	100	0	54	0	48	0	51	1.00
1739364--1739388	2	12.5	2	100	0	50	48	0	0	52	1.00
1745499--1745534	3	12.0	3	93	0	63	33	2	0	63	1.08
1753697--1753739	21	2.0	22	86	4	61	34	0	0	65	0.93
1756425--1756471	14	3.3	15	80	14	55	57	0	0	42	0.98

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21