genome.fa.s3.2.7.7.80.10.50.1000.30.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  30  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)
5539487--5539563	39	2.0	39	82	10	95	32	3	2	61	1.28
5539526--5539586	27	2.2	29	82	11	74	34	0	1	63	1.04
5540943--5540998	19	2.8	21	81	10	71	33	16	14	35	1.88
5540984--5541010	13	2.1	13	100	0	54	40	14	14	29	1.86
5543326--5543351	2	13.0	2	100	0	52	50	0	0	50	1.00
5559842--5559882	2	20.5	2	100	0	82	51	0	0	48	1.00
5561294--5561373	22	3.6	22	74	12	83	45	0	0	55	0.99
5566163--5566193	4	7.8	4	92	0	53	74	0	0	25	0.82
5567871--5567925	2	27.5	2	96	0	101	52	0	47	0	1.00
5569026--5569050	13	1.9	13	100	0	50	80	0	20	0	0.72
5569786--5569825	2	20.0	2	94	0	71	52	0	47	0	1.00
5573445--5573478	13	2.6	13	80	0	50	52	0	2	44	1.16
5574061--5574125	32	2.0	33	82	8	80	41	0	0	58	0.98
5574059--5574130	17	4.2	17	77	10	65	43	1	0	55	1.08
5577241--5577277	2	18.5	2	100	0	74	48	0	0	51	1.00
5577499--5577554	19	2.9	21	75	21	59	37	0	1	60	1.07
5582092--5582123	2	16.5	2	93	6	57	50	0	0	50	1.00
5585292--5585327	2	18.5	2	94	5	65	50	0	0	50	1.00
5585756--5585783	2	14.0	2	100	0	56	50	0	0	50	1.00
5587842--5587876	2	17.5	2	100	0	70	51	48	0	0	1.00
5588211--5588260	2	25.0	2	100	0	100	50	0	0	50	1.00
5601978--5602007	2	15.0	2	92	0	51	0	53	0	46	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5606047--5606091	19	2.4	19	85	3	56	55	11	6	26	1.59
5610781--5610815	14	2.8	12	84	16	52	37	0	0	62	0.95
5610785--5610838	16	3.4	16	82	12	60	33	1	0	64	1.04
5611492--5611522	16	1.9	16	93	0	53	45	0	0	54	0.99
5612184--5612212	3	9.7	3	100	0	58	68	0	0	31	0.89
5614171--5614196	2	13.0	2	100	0	52	0	50	0	50	1.00
5614196--5614227	2	16.0	2	100	0	64	50	0	0	50	1.00
5616339--5616395	29	2.0	29	85	0	78	42	0	0	57	0.98
5618272--5618307	12	3.0	12	95	0	63	25	11	0	63	1.27
5618866--5619073	110	1.9	112	87	9	311	38	9	3	48	1.52
5619665--5619727	22	2.9	22	71	17	58	39	1	6	52	1.37
5624558--5624587	15	2.0	15	93	0	51	63	0	0	36	0.95
5626001--5626025	7	3.6	7	100	0	50	12	0	0	88	0.53
5626264--5626336	36	2.0	36	84	10	96	61	1	0	36	1.05
5626264--5626333	13	5.8	12	74	15	63	62	1	0	35	1.04
5630166--5630197	2	16.0	2	100	0	64	50	0	0	50	1.00
5630292--5630354	2	31.5	2	100	0	126	49	0	0	50	1.00
5630904--5630941	11	3.5	11	85	10	51	21	0	7	71	1.11
5637270--5637301	16	2.0	16	100	0	64	37	25	0	37	1.56
5641438--5641533	45	2.1	45	100	0	192	38	0	22	38	1.55
5644445--5644484	13	3.1	13	89	7	55	32	7	0	60	1.25
5644911--5644949	19	2.1	19	85	9	53	35	0	0	64	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5644911--5644949	18	2.1	19	85	4	53	35	0	0	64	0.94
5645189--5645244	29	1.9	29	88	0	85	41	0	1	57	1.09
5645326--5645364	16	2.4	16	80	12	53	69	5	0	25	1.09
5645306--5645365	24	2.5	23	81	7	75	68	3	0	28	1.05
5646434--5646475	15	2.8	15	79	13	50	42	0	0	57	0.99
5651678--5651706	2	14.5	2	100	0	58	48	0	0	51	1.00
5664624--5664653	2	15.0	2	100	0	60	50	0	0	50	1.00
5667234--5667291	25	2.3	25	88	5	82	39	1	0	58	1.08
5678382--5678425	19	2.3	19	100	0	88	31	15	11	40	1.83
5681284--5681686	36	11.3	36	79	4	404	33	24	12	29	1.93
5681577--5682280	198	3.6	197	78	5	551	31	24	13	30	1.93
5681897--5682070	36	4.8	36	81	0	168	33	22	11	32	1.90
5681893--5682530	72	8.6	71	70	11	309	33	23	11	31	1.90
5682137--5682484	36	9.7	35	75	6	137	34	24	10	30	1.89
5681936--5682505	217	2.5	217	80	9	589	33	23	11	31	1.90
5682218--5682545	36	9.1	34	74	9	129	33	24	10	31	1.89
5682232--5682493	145	1.8	145	81	3	330	34	25	10	29	1.90
5684150--5684187	20	2.0	19	85	10	51	55	5	28	10	1.56
5684448--5684504	18	3.2	18	75	12	55	64	0	1	33	1.04
5684453--5684495	16	2.7	16	83	16	54	69	0	0	30	0.88
5685276--5685334	11	5.7	11	73	15	54	32	1	1	64	1.13
5685276--5685333	5	11.4	5	77	15	57	32	1	1	63	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5685272--5685342	35	2.0	35	89	8	108	33	1	1	63	1.12
5687690--5687715	3	8.7	3	100	0	52	65	0	0	34	0.93
5688962--5689001	21	2.0	20	95	5	71	42	0	0	57	0.98
5688962--5689009	21	2.5	19	87	12	64	43	0	0	56	0.99
5692491--5692551	30	2.0	30	96	0	113	57	13	4	24	1.56
5693619--5693663	6	7.5	6	97	0	72	33	40	15	11	1.83
5704650--5704713	6	9.8	6	77	15	56	65	3	0	31	1.08
5720668--5720985	158	2.0	158	94	2	559	36	18	10	35	1.85
5723980--5724029	2	25.0	2	91	0	82	46	0	4	50	1.20
5727539--5727563	13	1.9	13	100	0	50	36	16	16	32	1.90
5727519--5727585	33	2.0	33	88	0	98	32	11	14	40	1.83
5734111--5734155	23	2.0	24	83	12	60	35	0	0	64	0.94
5737593--5737626	2	17.0	2	93	0	59	52	0	0	47	1.00
5745509--5745645	68	2.0	68	100	0	274	34	13	24	27	1.93
5746122--5746189	36	1.9	36	84	3	93	22	17	5	54	1.64
5748223--5748310	42	2.1	42	97	0	167	25	23	25	26	2.00
5749654--5749972	159	2.0	159	93	3	554	36	18	10	34	1.85
5752955--5753006	2	26.0	2	92	0	86	46	0	3	50	1.20
5756518--5756542	13	1.9	13	100	0	50	36	16	16	32	1.90
5756498--5756564	33	2.0	33	88	0	98	32	11	14	40	1.83
5763092--5763137	24	2.0	25	83	12	62	34	0	0	65	0.93
5766576--5766611	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)
5778682--5778707	12	2.2	12	100	0	52	30	0	7	61	1.24
5778720--5778774	22	2.5	22	81	0	65	30	1	29	38	1.68
5778741--5778806	34	1.9	34	93	0	114	21	3	37	37	1.69
5780052--5780104	24	2.2	24	82	0	61	32	7	18	41	1.79
5782684--5782767	34	2.5	35	88	5	136	30	2	28	38	1.70
5782871--5782896	12	2.2	12	100	0	52	30	7	7	53	1.57
5784736--5785114	205	1.9	202	93	1	650	30	13	23	31	1.94
5785585--5785888	150	2.0	150	98	0	581	36	10	21	31	1.87
5786407--5786434	13	2.2	13	100	0	56	25	25	0	50	1.50
5786477--5786555	39	2.0	39	90	0	122	40	18	8	31	1.82
5788330--5788385	24	2.3	24	87	0	85	32	8	17	41	1.81
5791721--5791748	5	5.6	5	100	0	56	39	42	17	0	1.50
5792721--5792752	3	10.7	3	93	0	55	31	0	3	65	1.08
5804001--5804033	2	16.5	2	93	0	57	51	0	48	0	1.00
5804122--5804157	2	18.0	2	94	0	63	0	47	2	50	1.15
5804814--5804845	13	2.5	13	94	0	55	53	3	0	43	1.16
5816548--5816591	19	2.3	19	84	7	54	63	2	4	29	1.26
5822713--5822773	31	2.0	30	90	9	97	55	0	0	44	0.99
5822724--5822817	14	6.1	15	67	18	52	57	0	1	41	1.06
5823374--5823425	21	2.5	21	72	12	52	59	1	0	38	1.08
5823424--5823452	9	3.3	9	95	4	51	17	0	0	82	0.66
5823503--5823539	10	3.8	10	86	13	51	54	0	2	43	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5826293--5826383	41	2.2	40	80	7	103	49	1	0	49	1.08
5826323--5826383	20	3.0	21	79	11	72	52	0	0	47	1.00
5827110--5827163	11	5.1	11	75	20	53	66	0	0	33	0.92
5827182--5827244	33	2.0	32	90	6	101	53	0	3	42	1.16
5827188--5827245	18	3.4	18	71	23	54	55	0	1	43	1.10
5827216--5827254	20	2.1	18	85	9	51	58	0	0	41	0.98
5827188--5827253	32	2.1	32	82	5	80	57	0	1	40	1.08
5827735--5827773	19	1.9	19	85	10	51	51	0	2	46	1.14
5828212--5828237	4	6.5	4	100	0	52	23	0	0	76	0.78
5828284--5828317	2	17.0	2	100	0	68	0	50	0	50	1.00

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