genome.fa.s105.2.7.7.80.10.50.1000.10.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: Scaffold105
Parameters: 2 7 7 80 10 50 1000
Length:  2918491

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

This is table  10  of  16  ( 1849 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)
1542252--1542365	29	3.9	29	74	16	108	51	0	7	40	1.35
1555523--1555551	12	2.3	13	94	5	51	13	0	0	86	0.58
1557009--1557044	3	12.0	3	93	0	63	30	0	2	66	1.06
1558518--1558543	3	8.7	3	100	0	52	34	0	0	65	0.93
1559014--1559094	41	2.1	38	83	6	99	58	0	1	40	1.06
1559014--1559094	39	2.0	40	81	11	96	58	0	1	40	1.06
1559059--1559112	25	2.2	24	87	9	74	51	0	0	48	1.00
1559134--1559195	18	3.4	19	77	20	69	58	1	0	40	1.08
1559139--1559193	19	3.2	17	80	12	67	60	0	0	40	0.97
1559230--1559275	3	15.3	3	100	0	92	32	0	0	67	0.91
1559542--1559567	2	13.0	2	100	0	52	50	0	0	50	1.00
1561031--1561076	18	2.4	19	80	16	51	60	0	0	39	0.97
1561901--1562009	14	7.6	14	69	20	66	58	2	0	38	1.12
1561901--1562009	26	3.9	26	73	18	94	58	2	0	38	1.12
1561898--1561940	21	2.0	21	82	8	52	62	0	0	37	0.95
1561908--1561972	12	5.2	12	78	14	60	60	0	0	40	0.97
1562021--1562068	7	7.0	7	76	4	53	41	0	0	58	0.98
1562024--1562065	20	2.1	20	100	0	84	42	0	0	57	0.99
1562672--1562700	6	4.8	6	100	0	58	0	31	0	68	0.89
1576556--1576611	20	2.8	20	77	2	67	53	0	1	44	1.11
1576682--1576750	18	3.9	18	73	19	65	46	1	0	52	1.09
1576680--1576802	43	2.8	42	73	16	99	44	0	0	53	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1576772--1576811	15	2.7	15	88	3	55	47	2	0	50	1.14
1577703--1577747	18	2.5	19	83	16	60	68	2	0	28	1.01
1577688--1577744	28	2.1	27	87	9	80	68	1	0	29	1.00
1577705--1577746	11	3.8	11	81	6	50	69	2	0	28	1.01
1577906--1577934	13	2.2	13	100	0	58	41	0	6	51	1.28
1578723--1578768	17	2.7	17	86	0	65	34	4	0	60	1.16
1579128--1579169	19	2.2	19	86	0	57	57	2	0	40	1.12
1579883--1579963	27	3.1	27	75	16	80	51	1	2	44	1.22
1580472--1580513	20	2.0	22	86	9	61	52	0	0	47	1.00
1581354--1581378	2	12.5	2	100	0	50	52	0	0	48	1.00
1582021--1582104	33	2.6	33	79	11	93	50	2	0	47	1.14
1582050--1582110	17	3.6	17	72	16	56	52	1	0	45	1.10
1582121--1582176	29	2.0	28	86	10	78	57	1	0	41	1.09
1582590--1582617	2	14.0	2	100	0	56	50	0	0	50	1.00
1582651--1582711	24	2.4	25	79	15	72	27	0	3	68	1.05
1582671--1582704	12	2.7	13	86	4	52	26	0	0	73	0.83
1584808--1584845	20	1.9	20	89	10	60	55	0	0	44	0.99
1584805--1584855	21	2.5	20	72	15	50	52	0	0	47	1.00
1585053--1585093	3	13.7	3	100	0	82	31	0	0	68	0.90
1590254--1590286	2	16.5	2	100	0	66	48	0	0	51	1.00
1592281--1592377	27	3.5	26	78	17	99	40	0	1	58	1.05
1592304--1592481	5	36.6	5	67	19	83	42	0	0	57	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1592698--1592731	16	2.2	15	89	5	50	47	0	0	52	1.00
1592692--1592743	23	2.3	22	81	15	61	42	0	0	57	0.98
1592739--1592789	17	3.2	16	75	22	54	35	0	0	64	0.94
1592687--1592789	31	3.4	30	73	16	88	39	0	0	60	0.97
1596628--1596662	2	17.5	2	93	0	61	0	45	0	54	0.99
1606030--1606082	2	27.5	2	92	7	92	47	0	52	0	1.00
1609388--1609437	24	2.1	24	81	7	57	30	6	10	54	1.58
1609575--1609613	2	19.5	2	83	0	51	43	0	5	51	1.24
1611436--1611504	2	34.5	2	78	11	70	43	1	4	50	1.30
1612412--1612438	2	13.5	2	100	0	54	51	0	48	0	1.00
1614915--1614975	29	2.0	30	81	12	72	42	1	3	52	1.27
1619421--1619472	18	3.0	17	78	15	52	73	0	11	15	1.11
1619775--1619842	21	3.5	20	82	7	77	16	14	0	69	1.20
1623157--1623239	22	3.2	28	73	22	83	40	1	0	57	1.06
1626361--1626398	18	2.1	18	90	9	60	65	0	0	34	0.93
1626922--1626985	25	2.5	26	85	7	96	50	0	0	50	1.00
1626951--1626995	21	2.3	19	84	7	54	57	0	0	42	0.98
1627146--1627182	2	18.5	2	100	0	74	48	0	0	51	1.00
1627341--1627396	18	3.1	18	78	0	67	48	0	0	51	1.00
1627419--1627468	24	2.1	24	85	7	66	54	2	0	44	1.11
1627486--1627566	25	3.3	24	74	19	78	53	0	1	45	1.08
1627544--1627615	27	2.7	27	78	20	71	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)
1627564--1627615	24	2.2	24	83	13	63	50	0	0	50	1.00
1628327--1628368	15	2.6	16	77	7	50	30	0	0	69	0.89
1628345--1628450	22	4.7	21	73	20	72	42	1	0	55	1.10
1628389--1628456	21	3.2	21	82	15	79	45	2	0	51	1.16
1628347--1628466	21	5.3	23	68	20	74	42	1	0	55	1.09
1629382--1629416	15	2.2	16	90	5	54	2	0	14	82	0.77
1635290--1635380	5	18.4	5	67	22	50	38	1	1	59	1.12
1635290--1635340	13	3.7	13	79	10	57	33	1	0	64	1.05
1635321--1635394	22	3.1	23	74	16	69	45	0	1	52	1.09
1635596--1635633	2	19.0	2	94	0	67	47	0	2	50	1.15
1643716--1643785	29	2.4	29	80	4	79	67	7	8	17	1.40
1643720--1643785	28	2.3	29	82	10	82	66	7	9	16	1.42
1644487--1644528	2	21.0	2	90	0	66	45	0	50	4	1.23
1645289--1645314	2	13.0	2	100	0	52	50	0	0	50	1.00
1645469--1645514	15	2.8	17	80	12	60	50	0	4	45	1.21
1657022--1657054	17	1.9	17	93	0	57	69	3	9	18	1.28
1657690--1657741	24	2.2	24	86	10	72	38	11	19	30	1.87
1658616--1658656	21	1.9	22	85	5	57	48	7	0	43	1.30
1659484--1659611	28	4.5	26	71	21	82	56	0	0	42	1.10
1659487--1659553	24	2.7	25	81	11	75	53	0	1	44	1.09
1659520--1659574	17	3.4	17	75	25	64	56	0	0	43	0.99
1659884--1659925	22	2.0	21	86	9	59	59	0	21	19	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1662875--1662923	17	3.0	15	80	16	53	44	0	0	55	0.99
1662885--1662934	21	2.6	20	82	14	61	46	0	0	54	1.00
1664004--1664098	8	12.5	8	73	17	62	61	1	0	37	1.03
1664007--1664098	14	6.6	14	70	17	59	60	1	0	38	1.04
1664008--1664066	18	3.1	19	74	13	57	64	1	0	33	1.04
1664004--1664097	33	2.7	34	77	19	97	60	1	0	38	1.04
1664581--1664644	33	1.9	34	84	15	89	50	0	0	50	1.00
1665961--1666012	24	2.1	26	85	7	72	36	0	0	63	0.95
1666268--1666321	21	2.6	20	77	8	54	40	1	1	55	1.21
1667692--1667747	22	2.5	22	72	13	60	60	1	0	37	1.07
1667695--1667763	20	3.2	21	72	10	59	59	1	0	39	1.06
1668250--1668289	21	2.0	20	90	5	62	17	0	15	67	1.23
1668324--1668353	16	1.9	15	93	6	51	83	0	0	16	0.65
1668543--1668588	18	2.5	18	82	13	58	41	0	0	58	0.98
1669602--1669635	2	17.0	2	100	0	68	50	0	0	50	1.00
1674910--1674937	2	14.0	2	100	0	56	50	0	0	50	1.00
1675096--1675166	28	2.5	28	77	8	74	40	1	1	56	1.17
1675107--1675168	29	2.2	28	82	8	72	37	1	1	59	1.17
1675107--1675161	28	1.9	28	85	10	76	41	1	0	56	1.10
1677874--1677930	30	1.9	30	85	7	80	36	5	3	54	1.40
1678636--1678663	14	2.0	14	100	0	56	28	7	28	35	1.84
1678908--1678939	15	2.1	16	94	5	57	6	28	15	50	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1679096--1679141	23	2.0	23	82	0	56	47	0	0	52	1.00
1679126--1679166	19	2.2	19	86	8	57	63	2	0	34	1.08
1682663--1682709	23	2.0	23	87	4	67	55	2	0	42	1.12
1682682--1682732	26	2.0	26	84	7	68	60	0	1	37	1.08
1686032--1686088	22	2.4	23	80	16	64	38	0	1	59	1.08
1686057--1686168	33	3.4	32	73	17	86	40	0	0	58	1.04
1690430--1690467	2	19.0	2	100	0	76	50	0	50	0	1.00
1691221--1691280	28	2.1	28	90	0	93	35	8	20	36	1.82
1698309--1698343	18	1.9	18	88	11	54	80	2	5	11	1.00
1699400--1699435	17	2.1	17	90	10	56	61	0	0	38	0.96

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