genome.fa.s258.2.7.7.80.10.50.1000.18.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: Scaffold258
Parameters: 2 7 7 80 10 50 1000
Length:  5730937

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   

This is table  18  of  25  ( 2900 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)
4218466--4218496	10	3.1	10	100	0	62	38	0	0	61	0.96
4221220--4221250	2	15.5	2	100	0	62	51	0	0	48	1.00
4221708--4221752	2	22.5	2	100	0	90	48	0	0	51	1.00
4227291--4227350	23	2.6	23	84	7	68	41	0	0	58	0.98
4227287--4227352	11	5.8	12	70	22	54	42	0	0	57	0.98
4227704--4227756	21	2.5	21	76	8	54	39	0	0	60	0.97
4229562--4229595	17	2.0	17	88	11	52	35	2	2	58	1.28
4234557--4234606	14	3.6	14	78	10	57	62	4	4	30	1.32
4234557--4234612	29	2.0	29	89	3	87	60	3	3	32	1.31
4234664--4234699	17	2.2	17	90	5	56	27	0	2	69	1.02
4234649--4234702	26	2.1	25	86	10	74	27	0	1	70	0.98
4234944--4234977	16	2.2	15	89	5	50	44	0	0	55	0.99
4235175--4235222	17	2.9	17	77	17	57	41	0	0	58	0.98
4235217--4235258	22	1.9	22	85	9	59	61	2	0	35	1.09
4239829--4239858	2	15.0	2	100	0	60	50	0	0	50	1.00
4245024--4245198	89	2.0	89	94	1	305	53	3	8	35	1.47
4246662--4246694	2	16.5	2	100	0	66	51	0	0	48	1.00
4247775--4247830	21	2.6	22	73	18	55	46	0	3	50	1.19
4247810--4247893	42	2.0	43	81	6	100	50	1	1	47	1.16
4248826--4248858	2	16.5	2	100	0	66	0	51	0	48	1.00
4252442--4252477	2	18.0	2	100	0	72	50	0	0	50	1.00
4255328--4255375	2	24.0	2	100	0	96	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4262195--4262228	17	1.9	17	94	5	59	67	0	0	32	0.91
4263088--4263143	25	2.3	24	81	3	67	58	0	5	35	1.21
4264915--4264965	20	2.7	20	82	8	63	54	11	0	33	1.37
4288061--4288086	13	2.0	13	100	0	52	23	23	23	30	1.99
4290237--4290292	29	1.9	29	82	13	71	50	0	1	48	1.11
4290547--4290588	18	2.3	19	91	4	68	35	4	0	59	1.19
4291458--4291491	2	17.0	2	93	0	59	52	0	47	0	1.00
4292248--4292287	2	20.0	2	94	0	71	0	52	0	47	1.00
4293125--4293169	18	2.6	18	85	3	65	40	0	0	60	0.97
4293111--4293177	21	3.3	21	74	20	70	41	0	0	58	0.98
4297518--4297588	31	2.5	27	86	9	88	53	0	1	45	1.09
4306620--4306657	13	2.9	13	88	0	58	36	2	2	57	1.26
4314961--4315005	23	1.9	23	82	13	56	42	0	2	55	1.12
4315021--4315106	35	2.5	35	81	7	95	44	0	1	54	1.07
4315348--4315390	19	2.2	20	88	12	63	51	2	0	46	1.13
4315495--4315528	17	2.0	17	94	0	59	44	0	0	55	0.99
4318909--4318990	37	2.2	37	87	6	114	46	9	2	41	1.50
4321938--4321977	2	20.5	2	84	5	55	50	2	2	45	1.28
4322977--4323039	19	3.3	19	75	16	58	42	0	0	57	0.99
4323007--4323067	27	2.3	27	88	8	97	42	0	0	57	0.98
4324226--4324250	13	1.9	13	100	0	50	8	12	0	80	0.92
4326359--4326386	2	14.0	2	100	0	56	0	50	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4326386--4326416	2	15.5	2	100	0	62	48	0	0	51	1.00
4332296--4332334	2	20.0	2	94	5	71	51	0	48	0	1.00
4338445--4338507	27	2.3	28	75	8	67	42	4	3	49	1.39
4341006--4341045	21	2.0	20	85	5	53	45	0	0	55	0.99
4341344--4341395	21	2.5	22	74	22	58	55	1	0	42	1.10
4341369--4341504	68	2.0	69	82	7	170	47	5	2	43	1.42
4351492--4351539	24	2.0	24	95	0	87	31	16	10	41	1.82
4358804--4358848	18	2.7	17	86	10	58	46	2	2	48	1.26
4359021--4359208	48	3.9	48	90	1	288	26	13	36	23	1.92
4359020--4359208	95	2.0	96	90	1	299	26	13	36	23	1.92
4360545--4360569	2	12.5	2	100	0	50	48	0	0	52	1.00
4360823--4360862	2	20.0	2	100	0	80	50	0	0	50	1.00
4361756--4361795	2	20.0	2	84	0	53	42	0	2	55	1.13
4365333--4365359	2	13.5	2	100	0	54	0	48	0	51	1.00
4369932--4370076	1	145.0	1	97	0	272	0	98	0	0	0.12
4375999--4376023	6	4.2	6	100	0	50	0	52	0	48	1.00
4376463--4376576	34	3.1	39	69	24	95	44	3	0	51	1.18
4377252--4377277	2	13.0	2	100	0	52	50	0	0	50	1.00
4387217--4387257	21	1.9	22	95	5	75	56	0	4	39	1.21
4387620--4387659	2	20.0	2	100	0	80	0	50	0	50	1.00
4391580--4391783	104	2.0	104	99	0	399	34	8	18	38	1.82
4392464--4392504	2	20.5	2	100	0	82	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)
4393282--4393326	21	2.1	21	84	8	56	44	0	8	46	1.34
4394480--4394786	153	2.0	153	98	0	587	37	23	16	22	1.93
4399908--4399952	19	2.3	21	75	21	53	57	0	0	42	0.98
4400685--4400714	2	15.0	2	100	0	60	50	0	0	50	1.00
4401371--4401408	2	19.5	2	94	5	69	50	0	0	50	1.00
4401390--4401467	27	2.8	29	75	11	81	43	2	0	53	1.14
4403874--4403900	12	2.2	12	100	0	54	7	0	0	92	0.38
4403870--4403908	20	2.0	20	84	0	51	12	5	0	82	0.83
4405443--4405492	25	2.0	25	84	4	64	30	6	2	62	1.31
4407888--4407920	2	16.5	2	100	0	66	51	0	0	48	1.00
4408623--4408652	2	15.5	2	93	6	53	50	0	0	50	1.00
4409068--4409093	3	8.7	3	100	0	52	30	0	0	69	0.89
4409695--4409744	25	2.0	25	84	3	66	28	4	16	52	1.61
4413590--4413614	5	5.0	5	100	0	50	60	0	20	20	1.37
4415528--4415580	3	17.7	3	100	0	106	66	0	0	33	0.92
4416542--4416566	3	8.3	3	100	0	50	32	0	0	68	0.90
4421869--4421933	23	2.9	23	70	6	62	47	0	6	46	1.27
4422007--4422066	20	3.0	20	82	7	59	58	0	0	41	0.98
4422033--4422106	20	3.5	20	77	15	60	50	0	1	48	1.09
4426138--4426171	17	2.0	17	100	0	68	47	5	5	41	1.52
4432402--4432433	2	16.0	2	93	0	55	46	0	3	50	1.17
4437575--4437612	18	2.1	19	90	5	60	65	5	2	26	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4443276--4443327	13	4.0	13	76	0	59	42	1	3	51	1.31
4448723--4448752	3	10.0	3	92	0	51	30	0	3	66	1.07
4448876--4448901	2	13.0	2	100	0	52	50	0	0	50	1.00
4449670--4449695	2	13.0	2	100	0	52	0	50	0	50	1.00
4450245--4450269	5	5.0	5	100	0	50	80	0	0	20	0.72
4450539--4450567	3	9.7	3	100	0	58	65	0	0	34	0.93
4451623--4451652	4	7.5	4	100	0	60	73	0	26	0	0.84
4459783--4459807	2	12.5	2	100	0	50	48	0	0	52	1.00
4460464--4460512	2	24.5	2	95	0	89	51	2	0	46	1.12
4463816--4463860	19	2.4	19	85	7	65	80	0	13	6	0.91
4465143--4465184	18	2.3	18	80	8	50	59	14	0	26	1.35
4481811--4481857	23	2.0	25	84	16	64	42	2	0	55	1.12
4481857--4481898	17	2.5	17	75	17	52	64	0	0	35	0.94
4483472--4483527	29	2.0	28	86	10	78	42	0	0	57	0.99
4484680--4484710	16	2.0	15	93	6	53	54	0	0	45	0.99
4492223--4492251	13	2.2	13	100	0	58	51	6	6	34	1.55
4492900--4492934	2	17.5	2	100	0	70	51	48	0	0	1.00
4494923--4494962	21	1.9	22	85	10	57	47	0	5	47	1.24
4500165--4500221	28	2.0	28	96	0	105	49	17	19	14	1.80
4505722--4505750	2	14.5	2	100	0	58	48	0	0	51	1.00
4506289--4506340	21	2.5	21	78	12	61	57	3	0	38	1.17
4509382--4509430	24	2.0	24	96	0	89	46	8	10	34	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4513931--4513985	25	2.2	25	78	15	60	63	0	0	36	0.95
4513975--4514008	16	2.1	16	89	10	52	44	2	0	52	1.16
4517759--4517817	18	3.4	18	70	21	54	45	0	1	52	1.10
4517743--4517827	41	2.2	39	81	14	95	43	0	1	55	1.07
4517782--4517831	25	2.0	24	84	3	64	44	0	2	54	1.11
4518867--4518906	2	20.5	2	94	5	73	50	0	0	50	1.00
4519021--4519059	17	2.3	17	90	0	60	46	2	7	43	1.46
4519103--4519143	17	2.5	17	88	7	59	46	0	0	53	1.00
4525492--4525574	40	2.1	40	100	0	166	12	30	28	28	1.92
4534448--4534537	45	2.0	45	97	0	171	23	13	28	34	1.92

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