genome.fa.s8.2.7.7.80.10.50.1000.28.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: Scaffold8
Parameters: 2 7 7 80 10 50 1000
Length:  6381039

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   
          33   

This is table  28  of  33  ( 3942 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)
5030749--5030816	21	3.3	20	75	19	68	54	0	0	45	0.99
5034452--5034494	13	3.2	13	80	12	52	51	0	0	48	1.00
5038407--5038435	2	14.5	2	100	0	58	48	0	0	51	1.00
5040400--5040442	9	4.8	9	91	0	68	48	0	51	0	1.00
5043825--5043857	2	16.5	2	93	0	57	51	3	0	45	1.16
5046180--5046214	2	17.5	2	100	0	70	0	0	48	51	1.00
5053841--5053874	17	2.0	17	100	0	68	47	29	11	11	1.76
5057757--5057782	2	13.0	2	100	0	52	50	0	0	50	1.00
5060703--5060776	27	2.7	27	83	4	96	45	17	9	27	1.79
5065266--5065343	27	2.9	28	78	3	88	46	20	6	26	1.75
5067574--5067621	9	5.2	9	80	14	62	41	0	0	58	0.98
5067574--5067645	33	2.1	37	82	15	91	37	0	1	61	1.05
5069001--5069037	2	18.5	2	94	0	65	48	0	0	51	1.00
5070193--5070267	30	2.6	29	77	12	82	41	2	2	53	1.29
5070237--5070290	23	2.3	23	84	6	65	42	1	3	51	1.30
5071787--5071853	14	5.0	14	69	8	50	32	1	0	65	1.02
5071814--5071875	28	2.2	28	85	5	81	37	0	3	59	1.13
5071866--5071895	14	2.1	14	93	0	51	50	3	0	46	1.18
5071913--5071974	20	3.1	20	70	21	58	33	0	0	66	0.92
5072323--5072394	36	2.0	37	83	8	94	44	0	2	52	1.15
5075712--5075767	25	2.1	27	84	12	73	62	0	1	35	1.06
5075724--5075835	27	4.4	26	72	17	101	58	0	1	40	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5075732--5075853	59	2.0	60	82	13	146	54	0	2	42	1.13
5075759--5075822	32	2.0	33	90	3	103	56	0	1	42	1.09
5075737--5075820	10	8.3	10	67	25	52	55	0	2	41	1.12
5075791--5075830	20	2.0	20	85	9	55	57	0	0	42	0.98
5076042--5076117	37	2.1	35	85	7	98	43	0	0	56	0.99
5076038--5076117	36	2.1	37	84	6	108	45	0	0	55	0.99
5077213--5077269	29	2.0	28	89	3	87	57	0	0	42	0.98
5077521--5077586	17	3.9	17	75	15	57	50	0	1	48	1.10
5077786--5077849	6	11.2	6	83	11	55	53	0	0	46	1.00
5079984--5080105	57	2.1	57	86	0	163	17	16	38	27	1.91
5083367--5083391	13	1.9	13	100	0	50	16	8	4	72	1.24
5084039--5084078	19	2.1	19	86	9	55	40	2	0	57	1.12
5084439--5084479	21	2.0	21	85	9	57	24	7	2	65	1.30
5085054--5085211	54	3.1	50	72	16	142	51	0	10	37	1.42
5087785--5087819	2	17.5	2	100	0	70	48	0	0	51	1.00
5087847--5087896	18	2.7	19	78	9	59	38	0	6	56	1.24
5088992--5089037	19	2.4	19	85	0	56	56	0	4	39	1.19
5089967--5090017	23	2.2	23	86	6	68	50	3	1	43	1.31
5089950--5090085	29	4.9	27	72	21	79	47	3	2	46	1.35
5090004--5090073	30	2.4	30	83	7	90	44	2	4	48	1.37
5089942--5090047	52	2.0	54	83	10	139	46	6	1	45	1.40
5090096--5090168	27	2.8	26	81	4	83	58	2	1	36	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5090096--5090150	26	2.1	26	89	3	83	65	3	0	30	1.10
5090269--5090342	26	2.7	27	80	17	82	50	0	0	50	1.00
5090290--5090338	21	2.3	21	89	10	73	53	0	0	46	1.00
5090319--5090359	17	2.4	17	84	11	57	46	0	0	53	1.00
5090759--5090809	24	2.0	24	85	7	66	66	1	1	29	1.13
5091900--5091939	19	2.0	20	90	4	64	65	0	0	35	0.93
5092163--5092200	15	2.6	14	84	8	58	68	0	0	31	0.90
5092837--5092876	18	2.2	18	95	0	71	60	0	0	40	0.97
5093102--5093156	30	1.9	30	85	7	78	54	0	0	45	0.99
5093127--5093202	31	2.4	34	76	17	81	50	0	1	48	1.09
5093956--5093991	13	2.8	13	95	0	63	83	0	0	16	0.65
5093956--5093992	7	5.6	7	84	9	51	83	0	0	16	0.64
5094287--5094334	25	1.9	25	86	0	69	64	0	0	35	0.94
5094412--5094444	13	2.8	12	86	13	50	69	0	6	24	1.10
5094855--5094918	15	4.4	15	73	13	62	46	0	0	53	1.00
5095312--5095359	4	12.8	4	91	4	66	0	20	0	79	0.74
5095581--5095611	2	16.0	2	93	6	55	51	0	0	48	1.00
5095879--5095912	15	2.3	15	89	0	50	61	0	5	32	1.20
5097289--5097491	103	2.0	103	86	1	282	23	23	16	36	1.94
5100615--5100676	9	6.6	9	71	10	52	30	0	1	67	1.00
5100995--5101099	48	2.1	52	79	10	121	48	0	0	50	1.07
5104067--5104109	13	3.3	13	84	9	52	48	0	4	46	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5111507--5111554	19	2.6	18	81	15	62	66	0	0	33	0.92
5111569--5111623	20	2.8	19	78	10	58	40	0	1	58	1.09
5113802--5113830	14	2.1	14	93	6	51	41	0	0	58	0.98
5114137--5114189	21	2.5	22	85	11	76	28	0	11	60	1.31
5117425--5117454	2	15.0	2	100	0	60	0	0	50	50	1.00
5119372--5119410	2	19.5	2	100	0	78	48	0	0	51	1.00
5120241--5120278	14	2.7	15	88	12	62	39	0	0	60	0.97
5120241--5120284	14	3.1	14	81	12	54	36	0	0	63	0.95
5120260--5120302	21	2.0	23	90	9	72	32	0	0	67	0.91
5120247--5120300	14	3.7	14	76	9	54	35	0	0	64	0.94
5121732--5121782	19	2.8	18	80	17	52	68	0	0	31	0.90
5127443--5127472	2	15.0	2	100	0	60	50	0	50	0	1.00
5131297--5131341	16	2.9	16	78	18	51	51	2	0	46	1.13
5132181--5132230	12	4.1	12	80	12	57	34	0	0	66	0.92
5132186--5132235	21	2.4	22	76	10	59	36	0	0	64	0.94
5134793--5134865	27	2.7	27	85	4	85	47	21	5	24	1.72
5139362--5139414	24	2.3	23	78	15	56	43	3	1	50	1.30
5139361--5139412	23	2.2	25	83	10	65	42	3	1	51	1.31
5140654--5140686	2	16.5	2	100	0	66	51	0	48	0	1.00
5142523--5142570	24	2.0	24	91	0	78	14	18	14	52	1.75
5142624--5142667	20	2.1	21	83	4	54	47	0	0	52	1.00
5144452--5144493	15	2.9	15	80	19	54	45	0	0	54	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5144506--5144555	25	1.9	27	84	8	68	38	2	2	58	1.21
5145814--5145850	2	18.5	2	94	0	65	48	0	2	48	1.15
5164177--5164235	2	29.5	2	92	0	91	0	50	0	49	1.00
5165282--5165308	2	13.5	2	100	0	54	0	51	0	48	1.00
5165820--5165862	21	2.0	22	86	4	61	16	9	13	60	1.58
5170532--5170570	2	19.5	2	100	0	78	48	0	0	51	1.00
5171393--5171437	22	2.0	22	83	16	56	68	0	2	28	1.01
5171378--5171434	25	2.3	25	77	17	64	64	0	1	33	1.04
5171399--5171485	32	2.7	33	83	5	106	62	0	2	35	1.08
5171428--5171495	32	2.1	31	89	5	100	57	0	1	41	1.08
5171459--5171514	19	3.0	19	75	12	62	62	0	0	37	0.95
5172197--5172221	13	1.9	13	100	0	50	28	24	0	48	1.52
5178186--5178235	2	25.5	2	83	4	66	52	4	0	44	1.20
5178905--5178945	14	3.0	14	76	16	50	68	0	0	31	0.90
5184200--5184275	39	1.9	39	86	0	107	31	14	28	25	1.95
5187232--5187305	19	3.7	19	75	12	60	45	1	0	52	1.09
5187415--5187466	18	2.7	19	85	8	61	59	1	0	38	1.08
5193959--5193998	19	2.1	19	86	9	55	45	0	0	55	0.99
5194002--5194040	13	2.8	14	88	7	53	64	0	2	33	1.08
5194419--5194447	2	14.5	2	100	0	58	0	48	0	51	1.00
5194633--5194657	2	12.5	2	100	0	50	48	0	0	52	1.00
5194655--5194681	4	6.8	4	100	0	54	25	0	0	74	0.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5194801--5194835	6	6.0	6	86	6	54	0	17	0	82	0.66
5199316--5199360	23	1.9	24	86	4	65	37	6	0	55	1.26
5204472--5204521	13	3.7	13	79	10	55	52	0	0	48	1.00
5205966--5205990	5	5.0	5	100	0	50	40	0	0	60	0.97
5206000--5206056	21	2.8	21	84	7	64	40	0	0	59	0.97
5206772--5207021	48	5.1	49	80	5	292	46	13	13	27	1.80
5207656--5207712	6	8.8	6	75	12	51	64	0	0	35	0.93
5207689--5207751	30	2.1	30	82	5	74	42	0	0	57	0.99
5207732--5207777	5	9.2	5	77	17	51	34	0	0	65	0.93
5207732--5207777	14	3.4	14	85	8	69	34	0	0	65	0.93

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   
          33