genome.fa.s38.2.7.7.80.10.50.1000.12.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: Scaffold38
Parameters: 2 7 7 80 10 50 1000
Length:  2073527

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

This is table  12  of  15  ( 1750 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)
1607690--1607732	19	2.3	19	84	8	52	67	0	0	32	0.91
1607659--1607733	28	2.6	28	79	12	73	61	0	4	34	1.15
1607691--1607732	10	4.2	10	81	9	50	69	0	0	30	0.89
1607810--1607875	19	3.3	19	81	8	69	68	0	0	31	0.90
1608420--1608445	4	6.5	4	100	0	52	0	46	26	26	1.53
1608663--1608692	15	2.1	15	93	6	53	33	0	0	66	0.92
1608963--1609009	23	2.0	23	87	0	67	40	0	0	59	0.97
1609727--1609758	2	16.0	2	100	0	64	50	0	0	50	1.00
1610879--1610950	24	3.1	21	71	23	56	40	0	2	56	1.13
1611033--1611061	2	15.0	2	92	7	51	48	0	0	51	1.00
1615520--1615553	16	2.1	16	100	0	68	55	5	14	23	1.61
1618991--1619050	27	2.2	28	88	8	88	33	1	3	61	1.22
1620695--1620723	15	1.9	15	100	0	58	44	0	13	41	1.44
1621052--1621083	2	16.0	2	93	0	55	53	0	0	46	1.00
1630606--1630640	3	11.7	3	100	0	70	31	0	0	68	0.90
1632014--1632047	16	2.1	16	100	0	68	35	20	5	38	1.77
1636975--1637005	14	2.2	14	94	0	53	32	0	0	67	0.91
1637199--1637251	14	3.9	14	77	5	54	35	5	0	58	1.22
1637199--1637260	11	4.8	13	74	24	51	33	4	0	61	1.17
1637212--1637261	11	4.1	13	78	19	54	34	2	0	64	1.05
1637775--1637806	9	3.6	9	95	0	55	78	0	0	21	0.76
1637921--1637959	19	2.1	19	95	0	69	41	0	0	58	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1644481--1644557	15	4.9	16	70	19	56	45	3	1	49	1.28
1645848--1645888	18	2.4	17	88	8	57	53	0	0	46	1.00
1645847--1645888	17	2.5	17	85	11	59	52	0	0	47	1.00
1645867--1645942	29	2.6	30	87	6	102	61	2	0	35	1.10
1645867--1645942	30	2.6	30	87	6	93	61	2	0	35	1.10
1646205--1646251	18	2.7	18	73	3	51	48	0	0	51	1.00
1646213--1646292	18	4.5	17	72	12	63	57	0	0	42	0.98
1646249--1646290	22	2.0	21	85	4	57	59	0	0	40	0.97
1646521--1646578	2	30.5	2	77	16	52	53	0	1	44	1.10
1646521--1646564	7	6.1	7	84	10	54	52	0	2	45	1.13
1646547--1646660	47	2.4	46	79	12	124	59	0	0	39	1.03
1646602--1646659	29	2.1	29	81	12	68	63	0	0	36	0.94
1648157--1648201	10	4.5	11	81	13	53	68	0	0	31	0.89
1648161--1648245	28	2.9	30	77	11	88	67	0	0	32	0.91
1648836--1648860	2	12.5	2	100	0	50	48	0	0	52	1.00
1650886--1650918	17	1.9	17	93	0	57	39	0	0	60	0.97
1652374--1652404	15	2.0	16	93	6	55	70	3	0	25	1.02
1653084--1653132	26	1.9	25	84	12	64	59	4	4	32	1.35
1653928--1653960	2	16.5	2	100	0	66	51	0	0	48	1.00
1661365--1661404	6	7.2	6	86	11	50	42	0	0	57	0.98
1661360--1661422	27	2.3	28	75	8	67	42	0	0	57	0.99
1661575--1661614	14	2.9	14	85	7	55	47	0	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1661701--1661732	2	16.5	2	93	6	57	50	0	0	50	1.00
1663052--1663084	2	16.5	2	100	0	66	0	48	0	51	1.00
1667281--1667316	2	18.0	2	100	0	72	0	50	0	50	1.00
1667316--1667359	2	22.0	2	86	9	63	47	2	2	47	1.27
1667791--1667829	3	13.0	3	100	0	78	33	0	0	66	0.92
1668018--1668050	5	6.8	5	93	6	59	84	0	0	15	0.61
1668017--1668054	14	2.8	14	92	4	60	84	0	0	15	0.63
1671367--1671399	15	2.2	15	100	0	66	39	21	6	33	1.78
1673596--1673684	19	4.6	18	70	25	65	33	0	0	66	0.92
1676630--1676657	7	4.0	7	100	0	56	85	0	0	14	0.59
1677722--1677764	15	2.9	15	76	13	52	37	0	0	62	0.95
1678010--1678065	27	2.0	30	86	10	82	64	3	0	32	1.11
1678071--1678171	16	6.7	15	68	18	50	56	2	2	37	1.30
1678040--1678161	48	2.5	49	74	17	121	58	2	2	36	1.25
1683502--1683565	13	5.2	12	70	18	51	51	1	4	42	1.32
1683718--1683748	10	3.1	10	95	0	53	0	54	0	45	0.99
1683784--1683810	2	13.5	2	100	0	54	0	51	0	48	1.00
1684259--1684305	19	2.6	17	78	15	51	63	0	0	36	0.94
1685430--1685467	18	2.2	17	82	13	51	28	5	2	63	1.30
1687215--1687250	11	3.3	11	88	0	54	52	0	0	47	1.00
1688575--1688601	14	1.9	14	100	0	54	66	0	0	33	0.92
1691442--1691479	20	1.9	20	84	10	51	7	26	10	55	1.61
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1692381--1692427	19	2.4	20	96	3	87	36	6	0	57	1.24
1694563--1694587	13	1.9	13	100	0	50	0	28	0	72	0.86
1695911--1695952	13	3.1	14	77	16	52	0	47	4	47	1.23
1697820--1697873	18	2.8	20	83	8	67	59	0	0	40	0.98
1700006--1700036	2	15.5	2	93	0	53	0	51	0	48	1.00
1703737--1703787	24	2.0	24	85	7	66	21	0	1	76	0.88
1706905--1706949	18	2.6	17	82	6	56	51	2	0	46	1.13
1715980--1716051	2	36.0	2	94	0	126	52	0	0	47	1.00
1716476--1716536	31	2.0	31	93	0	104	39	13	19	27	1.89
1717255--1717299	2	22.5	2	100	0	90	0	48	0	51	1.00
1717299--1717331	2	16.5	2	100	0	66	48	0	0	51	1.00
1718866--1718890	13	1.9	13	100	0	50	20	0	0	80	0.72
1719528--1719574	18	2.5	19	83	10	53	53	2	0	44	1.12
1719918--1719952	4	9.0	4	87	6	54	74	0	0	25	0.82
1720357--1720410	18	3.0	18	94	0	99	46	0	0	53	1.00
1720892--1720926	16	2.2	16	89	0	52	45	0	0	54	0.99
1724714--1724768	21	2.8	19	84	13	67	58	0	0	41	0.98
1724718--1724768	18	2.5	20	81	12	61	56	0	0	43	0.99
1728327--1728357	2	15.5	2	93	0	53	0	51	0	48	1.00
1728615--1728644	1	30.0	1	93	0	51	0	0	96	3	0.21
1732062--1732113	26	2.0	25	85	3	68	21	0	1	76	0.87
1735244--1735288	18	2.6	17	82	6	56	51	2	0	46	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1744320--1744391	2	36.0	2	94	0	126	52	0	0	47	1.00
1744515--1744565	15	3.4	15	76	17	52	54	0	17	27	1.43
1744515--1744566	14	3.6	14	80	15	52	53	0	17	28	1.44
1744819--1744879	31	2.0	31	93	0	104	39	13	19	27	1.89
1745575--1745620	2	23.5	2	95	4	85	0	47	0	52	1.00
1745620--1745651	2	16.5	2	93	6	57	46	0	0	53	1.00
1748484--1748518	2	17.5	2	100	0	70	48	0	0	51	1.00
1748831--1748892	30	2.0	31	82	14	76	46	0	0	53	1.00
1748834--1748972	72	2.0	71	82	13	171	48	2	0	49	1.13
1752998--1753041	21	2.0	22	83	12	56	38	0	0	61	0.96
1753250--1753313	33	1.9	34	84	9	87	51	1	3	43	1.26
1753438--1753478	20	2.1	19	86	4	55	58	0	4	36	1.20
1753426--1753514	24	4.0	23	72	19	71	51	2	3	42	1.30
1753724--1753759	18	2.1	17	89	5	54	66	2	0	30	1.06
1754691--1754733	22	2.0	22	90	9	70	41	2	0	55	1.12
1754833--1754857	12	2.1	12	100	0	50	60	0	0	40	0.97
1754821--1754854	16	2.1	16	94	5	59	61	0	0	38	0.96
1755335--1755386	25	1.9	26	85	14	70	55	0	0	44	0.99
1755335--1755387	27	2.0	25	82	13	63	56	0	0	43	0.99
1755842--1755909	21	3.4	21	73	15	63	39	0	1	58	1.07
1755875--1755913	20	2.0	19	85	14	53	38	0	0	61	0.96
1756037--1756066	11	2.7	11	89	0	51	36	0	0	63	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1756013--1756134	61	2.0	60	96	1	226	44	3	2	50	1.31
1756096--1756127	11	2.9	11	90	0	55	34	0	0	65	0.93
1757747--1757796	25	2.0	26	84	11	68	36	26	10	28	1.88
1760826--1760879	9	6.0	9	85	6	65	53	0	0	46	1.00
1760828--1760889	19	3.3	19	84	4	72	53	0	0	46	1.00
1768241--1768286	23	2.0	23	95	0	83	28	8	10	52	1.66
1773537--1773577	19	2.1	20	95	4	75	43	0	0	56	0.99
1773545--1773588	19	2.4	18	85	11	54	47	2	2	47	1.27
1775725--1775776	19	2.5	20	79	20	54	50	1	0	48	1.12
1785368--1785408	19	2.3	17	83	8	55	60	0	9	29	1.28

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