genome.fa.s3.2.7.7.80.10.50.1000.27.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: Scaffold3
Parameters: 2 7 7 80 10 50 1000
Length:  6198200

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   

This is table  27  of  32  ( 3795 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)
4742613--4742656	17	2.5	18	74	7	54	63	2	2	31	1.19
4747658--4747683	7	3.7	7	100	0	52	23	0	0	76	0.78
4748965--4749236	137	2.0	137	100	0	544	35	19	19	25	1.95
4751313--4751360	2	24.0	2	91	0	78	54	0	45	0	0.99
4758338--4758367	1	30.0	1	93	0	51	0	96	0	3	0.21
4758336--4758367	12	2.8	12	95	4	57	0	93	0	6	0.34
4761799--4761861	21	3.1	21	73	13	53	36	0	1	61	1.05
4762094--4762144	16	3.3	15	78	10	50	60	3	1	33	1.26
4763315--4763375	30	2.0	30	96	0	113	45	1	0	52	1.10
4763395--4763428	18	1.9	18	94	5	61	50	14	0	35	1.44
4763963--4764013	19	2.8	18	79	5	57	50	1	1	45	1.24
4774387--4774464	29	2.7	29	82	9	88	50	17	5	26	1.67
4777097--4777137	21	2.0	21	95	0	73	29	12	19	39	1.88
4782878--4782926	21	2.4	20	80	12	55	65	0	2	32	1.04
4782893--4782945	21	2.4	23	84	6	65	66	0	0	33	0.92
4782939--4782987	16	3.2	15	78	13	55	46	0	0	53	1.00
4782945--4782996	17	3.1	17	81	13	54	48	0	0	51	1.00
4783622--4783673	25	2.1	25	82	13	63	40	0	3	55	1.18
4783868--4783933	22	3.1	21	76	21	59	40	0	1	57	1.08
4783868--4783926	22	2.7	22	78	19	61	40	0	1	57	1.09
4784137--4784184	3	17.0	3	76	20	50	66	0	0	33	0.92
4784139--4784184	15	3.5	13	82	17	60	67	0	0	32	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4786179--4786212	16	2.1	17	94	5	61	67	0	26	5	1.13
4792472--4792501	2	15.0	2	100	0	60	50	0	50	0	1.00
4796058--4796090	2	16.5	2	93	0	57	0	0	45	54	0.99
4800129--4800173	15	3.1	15	81	15	58	42	0	0	57	0.98
4800862--4801120	50	5.2	50	94	0	448	28	21	19	30	1.98
4805513--4805771	50	5.2	50	94	0	448	28	21	19	30	1.98
4821668--4821696	11	2.6	11	100	0	58	93	0	6	0	0.36
4821660--4821696	12	3.2	12	88	7	58	91	2	5	0	0.48
4824008--4824036	13	2.3	13	94	5	51	31	3	0	65	1.09
4823961--4824068	53	2.0	54	96	1	200	38	9	1	50	1.45
4826876--4826945	35	2.0	35	100	0	140	37	8	17	37	1.80
4829423--4829453	15	2.1	15	93	0	53	74	0	0	25	0.82
4829449--4829492	15	2.9	16	86	13	74	52	0	0	47	1.00
4834221--4834247	2	13.5	2	100	0	54	51	0	0	48	1.00
4834268--4834331	33	1.9	33	93	0	110	37	14	10	37	1.81
4835008--4835032	2	12.5	2	100	0	50	52	0	0	48	1.00
4835032--4835063	2	16.0	2	100	0	64	50	0	50	0	1.00
4835229--4835258	15	2.0	15	93	0	51	53	0	10	36	1.35
4852131--4852173	17	2.4	18	88	3	61	58	0	0	41	0.98
4852647--4852695	21	2.2	22	78	10	55	55	0	2	42	1.11
4852683--4852737	18	2.9	19	76	15	53	47	1	1	49	1.23
4853889--4853938	23	2.3	21	83	12	66	4	14	0	82	0.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4853891--4853938	22	2.2	21	88	7	69	2	14	0	83	0.74
4853895--4853939	14	3.3	14	84	3	56	2	17	0	80	0.82
4854400--4854431	7	4.4	7	92	7	55	37	0	0	62	0.95
4854400--4854431	15	2.2	15	94	5	57	37	0	0	62	0.95
4855519--4855553	17	1.9	19	88	11	56	65	2	0	31	1.07
4856257--4856281	2	12.5	2	100	0	50	48	0	0	52	1.00
4857936--4858001	27	2.6	25	79	13	71	48	3	0	48	1.17
4857941--4858006	26	2.5	26	80	7	80	48	3	0	48	1.17
4859262--4859386	27	4.6	25	68	14	70	56	0	0	42	1.04
4859265--4859386	29	4.5	28	70	15	85	55	0	0	43	1.05
4859291--4859402	8	14.0	8	69	21	58	57	0	0	41	1.05
4859282--4859386	39	2.6	40	75	10	99	56	0	0	43	0.99
4859285--4859390	29	3.4	31	81	10	101	56	0	0	43	0.99
4859297--4859391	18	5.9	16	76	21	67	57	0	0	42	0.98
4862408--4862436	3	9.7	3	100	0	58	0	31	0	68	0.89
4866941--4866979	20	2.0	20	85	10	53	43	2	2	51	1.29
4874761--4874785	13	1.9	13	100	0	50	60	0	0	40	0.97
4876086--4876173	31	2.9	31	80	8	94	54	0	0	45	0.99
4876417--4876522	24	4.3	24	73	14	83	66	0	0	33	0.92
4876436--4876478	5	8.0	5	85	14	59	74	0	0	25	0.82
4876428--4876584	18	8.7	18	68	21	73	64	0	0	34	1.03
4876418--4876582	11	15.3	11	67	18	53	64	0	0	33	1.02
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4883276--4883309	2	17.0	2	100	0	68	0	50	0	50	1.00
4883309--4883346	2	19.0	2	100	0	76	50	0	0	50	1.00
4889636--4889665	15	2.0	15	93	0	51	63	0	0	36	0.95
4897981--4898038	17	3.3	17	83	9	64	56	1	1	39	1.19
4898015--4898074	29	2.2	27	82	8	68	60	1	1	36	1.17
4913719--4913775	24	2.3	27	82	11	68	42	0	1	56	1.10
4917740--4917817	41	1.9	41	86	0	111	51	5	0	43	1.24
4917797--4917895	17	6.1	17	67	17	66	58	1	2	38	1.16
4917784--4917884	32	3.1	33	77	9	111	57	0	1	39	1.17
4918292--4918341	15	3.4	15	72	25	52	32	0	0	68	0.90
4918290--4918347	29	2.0	29	86	6	82	32	0	1	65	1.03
4918353--4918391	20	2.0	20	85	9	55	58	0	0	41	0.98
4918377--4918415	18	2.2	18	86	9	53	51	2	5	41	1.38
4918868--4918912	24	2.0	22	86	8	63	46	0	0	53	1.00
4918855--4918922	32	2.1	32	83	5	84	48	0	0	51	1.00
4922464--4922509	21	2.1	22	84	11	60	34	4	2	58	1.30
4924927--4924959	17	2.0	17	88	5	50	51	12	24	12	1.73
4938275--4938323	23	2.1	24	88	3	73	53	0	0	46	1.00
4938519--4938554	13	2.8	13	91	8	56	72	0	0	27	0.85
4945269--4945297	2	14.5	2	100	0	58	0	0	48	51	1.00
4945633--4945689	11	5.0	11	77	14	62	66	0	0	33	0.92
4945626--4945684	27	2.1	30	87	9	88	64	1	0	33	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4946014--4946051	15	2.5	15	83	12	51	42	0	0	57	0.98
4946216--4946242	2	13.5	2	100	0	54	48	0	0	51	1.00
4947358--4947403	22	2.0	24	91	8	78	30	0	0	69	0.89
4948003--4948033	3	10.3	3	100	0	62	32	0	0	67	0.91
4947961--4948104	74	1.9	74	97	0	270	26	13	6	52	1.66
4948077--4948104	3	9.3	3	100	0	56	32	0	0	67	0.91
4948817--4948878	32	2.0	31	87	3	88	51	1	0	46	1.10
4950555--4950589	14	2.4	15	85	4	54	62	14	17	5	1.49
4953689--4953735	18	2.5	19	83	12	62	59	0	0	40	0.97
4953693--4953740	20	2.3	20	85	3	60	58	0	0	41	0.98
4954104--4954211	53	2.0	53	90	0	171	22	28	10	38	1.86
4954293--4954321	13	2.1	14	93	6	51	58	0	0	41	0.98
4957631--4957659	10	2.7	11	89	10	51	27	10	0	62	1.28
4962089--4962113	2	12.5	2	100	0	50	52	48	0	0	1.00
4962113--4962139	2	13.5	2	100	0	54	51	0	0	48	1.00
4963696--4963735	2	20.0	2	89	0	62	47	2	0	50	1.14
4971286--4971315	2	15.0	2	100	0	60	50	0	0	50	1.00
4971940--4971988	25	1.9	26	87	4	73	40	12	0	46	1.41
4972121--4972153	16	2.0	17	88	5	50	63	9	0	27	1.24
4978669--4978697	2	14.5	2	100	0	58	0	48	0	51	1.00
4979132--4979218	44	2.0	44	88	4	131	56	5	3	34	1.40
4979556--4979588	11	2.8	12	86	9	50	69	24	6	0	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4983097--4983136	20	2.0	21	85	5	55	35	2	0	62	1.09
4983382--4983542	14	12.2	13	65	18	75	55	0	0	43	1.04
4983386--4983540	58	2.6	56	72	16	143	56	0	0	43	1.04
4983422--4983539	33	3.7	33	79	10	88	53	0	0	45	1.06
4983487--4983543	15	3.9	15	71	15	57	56	0	0	43	0.99
4983484--4983554	29	2.6	27	81	18	85	57	0	0	42	0.98
4983383--4983541	21	7.9	20	67	16	62	56	0	0	42	1.03
4983456--4983543	46	1.9	46	82	15	112	55	0	0	44	0.99
4983452--4983552	15	6.1	18	64	30	55	56	0	0	43	0.99
4987200--4987257	27	2.1	27	81	6	64	32	1	0	65	1.03

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32