genome.fa.s258.2.7.7.80.10.50.1000.23.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  23  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)
5335071--5335104	14	2.4	14	90	5	50	47	2	2	47	1.32
5335118--5335167	3	16.7	3	100	0	100	66	0	34	0	0.92
5337589--5337622	15	2.4	14	85	5	50	52	0	0	47	1.00
5337967--5337995	2	14.5	2	100	0	58	51	48	0	0	1.00
5340656--5340690	2	17.5	2	100	0	70	51	0	48	0	1.00
5342641--5342719	37	2.1	37	92	0	131	59	15	5	20	1.54
5344638--5344747	55	2.0	55	100	0	220	43	20	20	16	1.88
5345156--5345189	2	17.0	2	100	0	68	50	0	0	50	1.00
5347159--5347190	6	5.3	6	100	0	64	31	53	0	15	1.43
5351590--5351652	31	2.0	31	100	0	126	28	15	15	39	1.89
5351636--5351680	22	2.0	22	100	0	90	17	31	17	33	1.94
5352921--5352950	15	2.0	15	100	0	60	20	20	13	46	1.83
5355928--5355986	20	2.9	20	80	12	59	42	0	1	55	1.09
5358762--5358803	15	2.7	15	88	7	57	50	2	0	47	1.14
5361772--5361822	19	2.7	19	82	8	61	37	5	1	54	1.36
5368593--5368617	2	12.5	2	100	0	50	0	52	0	48	1.00
5369130--5369165	17	2.1	17	100	0	72	27	11	19	41	1.85
5369262--5369305	18	2.5	17	85	3	61	61	0	31	6	1.22
5373312--5373383	25	2.7	27	75	10	69	48	1	1	48	1.18
5373284--5373385	27	3.8	26	72	16	84	47	0	0	50	1.14
5373422--5373480	28	2.2	27	85	8	77	59	3	0	37	1.14
5377575--5377627	9	5.6	10	72	20	51	28	0	0	71	0.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5381319--5381357	17	2.4	17	82	4	53	48	0	0	51	1.00
5381932--5381964	7	4.9	7	85	7	50	84	0	0	15	0.61
5382673--5382719	8	5.8	8	82	9	51	4	85	6	4	0.84
5393560--5393593	16	2.1	16	88	0	50	44	0	0	55	0.99
5393649--5393702	6	9.0	6	79	18	51	31	0	1	66	1.02
5394914--5394972	22	2.6	23	81	13	77	59	0	5	35	1.20
5395796--5395828	6	5.3	6	92	7	57	36	0	0	63	0.95
5396004--5396070	24	2.7	25	74	6	64	49	0	2	47	1.16
5396706--5396755	25	2.0	26	84	7	68	14	4	10	72	1.26
5397128--5397178	17	3.1	17	83	10	54	62	0	0	37	0.95
5398483--5398526	17	2.6	17	81	0	61	6	9	4	79	1.04
5404070--5404127	27	2.1	27	83	0	71	56	0	1	41	1.09
5404346--5404378	2	16.5	2	100	0	66	51	0	0	48	1.00
5404422--5404465	20	2.2	20	84	11	56	29	0	0	70	0.88
5404750--5404784	2	17.5	2	100	0	70	48	0	0	51	1.00
5413336--5413373	18	2.3	17	86	13	53	36	5	18	39	1.73
5413336--5413378	18	2.7	15	80	16	50	41	4	18	34	1.71
5419791--5419839	19	2.6	18	83	6	62	71	2	0	26	0.97
5420767--5420833	16	3.5	20	72	23	65	59	0	0	40	0.97
5420749--5420845	13	6.9	14	69	19	53	59	0	0	40	0.97
5420708--5420845	8	15.9	8	69	23	59	61	2	0	36	1.08
5422021--5422066	18	2.6	18	86	13	76	39	0	0	60	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5422016--5422072	11	5.0	11	74	14	53	38	0	0	61	0.96
5422461--5422504	15	2.8	16	76	16	56	34	4	0	61	1.16
5423021--5423051	2	15.5	2	100	0	62	51	0	0	48	1.00
5423043--5423101	16	3.6	16	78	15	59	45	0	1	52	1.10
5423314--5423355	17	2.4	17	88	4	57	50	9	2	38	1.48
5424636--5424667	2	16.0	2	93	0	55	46	0	0	53	1.00
5428269--5428300	7	4.4	7	92	7	55	43	0	0	56	0.99
5431817--5431886	36	1.9	36	85	0	95	51	1	1	45	1.18
5432381--5432463	14	5.9	14	75	4	78	28	15	21	33	1.94
5432381--5432516	14	9.6	14	73	4	69	29	16	19	34	1.94
5432451--5432489	15	2.6	15	79	0	51	30	10	17	41	1.83
5435357--5435388	16	2.1	15	94	5	55	65	0	0	34	0.93
5435390--5435419	14	2.1	14	93	0	51	10	6	0	83	0.81
5440300--5440329	3	10.0	3	100	0	60	33	0	0	66	0.92
5442075--5442114	19	2.2	18	86	4	53	32	2	2	62	1.22
5442092--5442205	18	5.9	18	66	30	58	43	0	0	54	1.12
5442146--5442227	39	2.1	40	82	11	98	43	1	2	52	1.22
5442196--5442236	11	3.8	11	78	15	50	34	0	2	63	1.08
5446286--5446317	2	16.0	2	100	0	64	50	0	0	50	1.00
5450288--5450325	4	9.5	4	88	0	58	2	26	47	23	1.65
5452937--5452979	2	21.5	2	100	0	86	48	0	0	51	1.00
5458653--5458820	84	2.0	84	98	0	327	44	18	10	26	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5467920--5467997	23	3.3	23	78	12	70	50	1	0	48	1.09
5468235--5468272	19	2.0	19	85	10	51	39	2	0	57	1.12
5468526--5468574	26	1.9	25	91	4	80	36	0	2	61	1.08
5468561--5468594	10	3.3	10	87	4	50	47	0	0	52	1.00
5469111--5469158	2	24.0	2	100	0	96	50	0	0	50	1.00
5469215--5469276	30	2.0	31	84	9	83	40	3	0	56	1.15
5475836--5476135	165	1.8	165	84	4	408	32	27	17	23	1.96
5475836--5476185	165	2.1	165	81	5	395	33	27	16	22	1.95
5480474--5480526	24	2.3	22	83	9	61	26	28	13	32	1.93
5481256--5481320	32	2.0	34	90	6	107	16	27	9	46	1.78
5486999--5487040	2	20.0	2	90	9	50	47	7	0	45	1.30
5491248--5491283	16	2.2	16	90	9	56	55	0	2	41	1.14
5495698--5495728	14	2.2	14	94	0	53	80	9	6	3	0.99
5504128--5504165	19	2.0	19	85	10	51	39	2	0	57	1.12
5504451--5504484	10	3.3	10	87	4	50	47	0	0	52	1.00
5504503--5504535	17	1.9	17	93	0	57	57	0	6	36	1.23
5505066--5505100	8	4.2	8	85	7	52	28	0	0	71	0.86
5505066--5505100	17	2.1	16	89	5	52	28	0	0	71	0.86
5507411--5507450	19	2.1	19	90	4	62	45	0	0	55	0.99
5507416--5507459	19	2.2	20	88	4	63	52	0	0	47	1.00
5511692--5511991	165	1.8	165	84	4	417	32	27	18	22	1.97
5511692--5512041	165	2.1	165	82	5	404	33	27	17	22	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5516325--5516377	24	2.3	22	83	9	61	26	28	13	32	1.93
5517112--5517176	32	2.0	34	90	6	107	16	27	9	46	1.78
5522588--5522655	35	2.0	34	85	8	93	55	2	0	41	1.15
5522660--5522730	36	2.0	36	94	0	124	50	7	0	42	1.29
5524463--5524506	22	2.0	23	90	4	72	27	0	2	70	0.99
5524463--5524504	11	3.9	11	78	3	50	28	0	2	69	1.01
5524951--5524981	16	1.9	16	93	0	53	70	0	6	22	1.09
5525187--5525277	30	3.2	29	75	6	87	46	0	2	51	1.13
5525577--5525619	23	1.9	22	85	4	59	27	2	4	65	1.25
5525780--5525817	16	2.4	16	83	12	51	60	0	0	39	0.97
5529521--5529554	13	2.6	13	95	0	59	35	0	2	61	1.11
5532898--5533062	82	2.0	82	95	0	294	38	21	14	25	1.92
5535204--5535303	43	2.3	43	89	1	157	47	5	8	40	1.55
5536146--5536195	24	2.0	25	85	11	68	42	0	2	56	1.11
5536163--5536245	19	4.5	19	67	21	61	42	0	0	57	0.98
5536161--5536206	15	3.2	15	75	12	51	47	0	0	52	1.00
5536153--5536224	34	2.1	35	82	12	87	43	0	1	55	1.08
5536191--5536240	20	2.5	21	78	12	61	42	0	0	58	0.98
5536412--5536440	13	2.2	13	100	0	58	51	0	0	48	1.00
5536411--5536476	15	4.4	15	73	19	57	53	1	0	45	1.09
5536403--5536460	15	4.2	14	74	21	52	44	0	0	55	0.99
5536695--5536730	2	18.0	2	94	0	63	52	0	0	47	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5540398--5540442	3	15.0	3	95	0	81	33	35	0	31	1.58
5541882--5541922	15	2.6	17	75	25	54	53	0	0	46	1.00
5542210--5542272	25	2.3	28	81	10	69	58	0	3	38	1.14
5542263--5542312	24	2.2	23	86	10	68	40	2	0	58	1.10
5543069--5543208	25	5.5	25	69	19	85	56	2	4	37	1.31
5543083--5543132	22	2.1	25	82	17	63	60	0	0	40	0.97
5543164--5543202	19	2.0	20	85	14	55	56	0	5	38	1.22
5543456--5543485	2	15.0	2	100	0	60	50	0	0	50	1.00
5543958--5544021	30	2.1	31	82	8	78	46	3	1	48	1.27
5545925--5546007	42	2.0	42	85	4	114	39	4	16	38	1.70

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