genome.fa.s4.2.7.7.80.10.50.1000.20.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: Scaffold4
Parameters: 2 7 7 80 10 50 1000
Length:  5986281

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   

This is table  20  of  31  ( 3628 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)
4415537--4415573	14	2.5	15	86	8	58	43	0	0	56	0.99
4416537--4416588	19	2.9	17	78	13	50	32	1	0	65	1.04
4417276--4417304	2	14.5	2	100	0	58	48	0	51	0	1.00
4418434--4418543	28	3.9	28	76	20	88	58	0	0	40	1.11
4418448--4418513	34	1.9	34	85	11	91	62	1	0	36	1.05
4418460--4418524	22	3.0	23	78	13	66	58	1	0	40	1.07
4418461--4418549	34	2.7	32	80	16	85	57	1	0	41	1.06
4418463--4418549	28	3.0	29	81	11	90	56	1	0	42	1.07
4419068--4419103	17	2.0	19	89	10	58	38	0	0	61	0.96
4424099--4424130	16	2.0	16	93	0	55	46	28	0	25	1.53
4429820--4429848	4	7.2	4	100	0	58	24	0	0	75	0.80
4430137--4430181	22	2.1	21	84	15	58	68	4	0	26	1.08
4430523--4430602	34	2.3	36	87	8	114	58	1	1	38	1.14
4430546--4430601	24	2.3	24	75	6	60	60	0	1	37	1.07
4430582--4430641	24	2.4	25	81	16	70	50	0	3	46	1.18
4432041--4432093	27	2.0	27	84	0	70	26	1	52	18	1.56
4435364--4435392	3	9.7	3	100	0	58	34	0	0	65	0.93
4435772--4435839	33	2.1	31	81	10	75	51	0	1	47	1.09
4435782--4435828	24	1.9	24	83	12	60	48	0	2	48	1.13
4435781--4435862	25	3.5	23	74	21	64	47	0	1	51	1.08
4440083--4440116	2	18.0	2	88	11	54	50	0	0	50	1.00
4440089--4440122	16	2.1	16	88	0	50	47	2	2	47	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4440131--4440189	22	2.7	22	81	0	73	50	0	5	44	1.24
4441022--4441065	22	2.0	22	86	8	63	54	0	0	45	0.99
4442207--4442285	43	1.9	40	84	7	104	55	0	0	44	0.99
4442256--4442300	22	2.1	21	84	12	56	64	2	0	33	1.06
4443366--4443390	13	1.9	13	100	0	50	80	0	4	16	0.87
4447712--4447843	70	1.9	69	92	1	219	46	13	12	28	1.79
4449731--4449773	20	2.1	21	91	4	70	58	0	0	41	0.98
4449736--4449783	20	2.5	19	86	10	62	54	0	0	45	0.99
4452330--4452368	2	19.5	2	100	0	78	51	0	48	0	1.00
4452427--4452456	2	15.0	2	100	0	60	0	0	50	50	1.00
4454660--4454688	2	14.5	2	100	0	58	0	51	0	48	1.00
4456124--4456159	3	12.0	3	100	0	72	33	0	0	66	0.92
4457212--4457259	21	2.3	21	78	3	53	31	6	2	60	1.33
4457832--4457876	18	2.4	18	85	14	56	40	0	2	57	1.11
4458731--4458769	19	2.1	19	90	9	62	58	0	0	41	0.98
4464250--4464278	2	14.5	2	100	0	58	51	0	0	48	1.00
4467281--4467340	30	2.0	30	100	0	120	50	3	16	30	1.62
4470664--4470712	23	2.1	24	85	11	66	36	2	0	61	1.08
4472694--4472731	19	2.0	19	89	0	58	23	21	15	39	1.92
4474045--4474075	15	2.1	15	93	0	53	41	0	0	58	0.98
4476324--4476363	20	2.0	20	90	9	64	62	0	0	37	0.95
4479414--4479448	15	2.4	14	90	9	52	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4481175--4481244	34	2.1	34	97	0	131	25	20	1	52	1.54
4481633--4481657	3	8.3	3	100	0	50	68	0	0	32	0.90
4481658--4481699	3	14.0	3	100	0	84	33	0	0	66	0.92
4482254--4482297	2	22.0	2	95	0	79	47	0	2	50	1.13
4486356--4486397	14	3.1	14	80	10	52	33	0	7	59	1.25
4489941--4489976	18	1.9	19	88	5	56	33	2	0	63	1.08
4489967--4490008	20	2.0	21	86	4	59	52	0	0	47	1.00
4490996--4491043	2	24.0	2	100	0	96	50	0	0	50	1.00
4493011--4493045	17	2.0	18	88	5	54	45	0	2	51	1.16
4493831--4493870	20	2.0	20	90	0	62	27	0	22	50	1.50
4494023--4494077	2	27.5	2	83	7	67	49	1	1	47	1.23
4494006--4494054	21	2.4	21	83	6	57	55	0	0	44	0.99
4494157--4494194	2	19.0	2	100	0	76	0	0	50	50	1.00
4496138--4496204	21	3.2	21	78	17	70	53	0	0	46	1.00
4496457--4496488	2	16.0	2	100	0	64	50	0	0	50	1.00
4497520--4497587	32	2.1	31	82	15	77	58	1	1	38	1.16
4497531--4497618	41	2.2	40	83	6	115	54	1	1	43	1.15
4498325--4498366	17	2.3	18	80	19	52	57	0	0	42	0.99
4499569--4499601	12	2.9	12	86	13	52	21	0	0	78	0.75
4502291--4502320	2	15.0	2	100	0	60	50	0	0	50	1.00
4504058--4504105	18	2.6	18	83	3	60	54	0	0	45	0.99
4504085--4504110	11	2.4	11	100	0	52	65	0	0	34	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4507265--4507318	22	2.5	22	81	6	56	74	7	11	7	1.23
4507279--4507321	22	2.0	21	90	4	68	76	2	9	11	1.10
4508603--4508828	28	8.2	28	80	6	230	27	24	12	35	1.91
4508679--4508725	23	2.0	23	91	0	76	29	21	12	36	1.91
4508603--4508814	79	2.6	81	77	12	216	27	24	12	35	1.92
4508603--4508808	107	1.9	107	85	3	281	28	23	12	35	1.91
4509119--4509206	41	2.1	41	85	8	117	55	1	1	42	1.14
4509911--4509952	17	2.3	18	80	19	52	57	0	0	42	0.99
4510402--4510433	15	2.3	15	89	10	50	46	3	0	50	1.17
4510701--4510730	2	15.0	2	100	0	60	50	0	0	50	1.00
4510944--4510974	3	10.3	3	100	0	62	64	0	0	35	0.94
4511182--4511214	12	2.9	12	86	13	52	21	0	0	78	0.75
4512350--4512377	2	14.0	2	100	0	56	50	0	0	50	1.00
4512921--4512962	21	1.9	23	90	9	70	45	0	0	54	0.99
4512921--4512968	21	2.2	21	85	10	62	45	0	0	54	0.99
4517474--4517565	9	10.6	9	77	11	57	14	35	0	50	1.43
4519040--4519075	2	18.0	2	100	0	72	50	0	0	50	1.00
4519680--4519781	50	2.0	50	92	0	168	42	15	13	28	1.85
4520068--4520094	2	13.5	2	100	0	54	51	0	48	0	1.00
4523364--4523409	19	2.5	19	86	10	60	39	0	4	56	1.19
4530758--4530795	15	2.7	14	84	11	51	36	0	0	63	0.95
4531183--4531213	15	2.1	15	94	5	55	38	0	0	61	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4531440--4531478	2	19.5	2	100	0	78	0	51	0	48	1.00
4540402--4540435	2	17.0	2	100	0	68	50	0	0	50	1.00
4540773--4540811	2	19.5	2	100	0	78	48	0	0	51	1.00
4541058--4541087	2	15.0	2	100	0	60	50	0	50	0	1.00
4541115--4541154	13	3.1	13	81	0	53	65	2	0	32	1.06
4542255--4542316	10	6.1	10	85	10	72	46	1	8	43	1.42
4545393--4545426	2	17.0	2	100	0	68	50	0	0	50	1.00
4546964--4547000	4	8.8	4	91	8	56	21	2	0	75	0.92
4547529--4547570	17	2.4	18	81	18	54	66	0	2	30	1.04
4547652--4547746	48	1.9	51	85	6	133	58	1	1	38	1.12
4547696--4547741	19	2.5	18	78	3	56	60	0	2	36	1.09
4547543--4547868	158	2.1	157	80	11	355	54	2	3	39	1.30
4551033--4551077	12	3.9	12	78	18	51	42	0	0	57	0.98
4551215--4551239	4	6.2	4	100	0	50	28	0	0	72	0.86
4551993--4552032	19	2.0	20	85	4	55	47	5	2	45	1.38
4552241--4552278	19	2.1	18	90	5	58	55	0	0	44	0.99
4551815--4552591	286	2.7	282	77	10	794	42	5	7	43	1.58
4553977--4554007	2	15.5	2	93	0	53	48	0	3	48	1.17
4555928--4556014	39	2.2	39	82	8	97	18	12	22	45	1.83
4557896--4557937	21	1.9	21	85	9	57	59	0	0	40	0.97
4557896--4557950	23	2.3	23	79	17	60	54	0	1	43	1.10
4558002--4558040	19	2.1	19	85	9	53	58	0	0	41	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4559511--4559563	21	2.6	21	87	3	81	52	0	0	47	1.00
4560742--4560770	2	14.5	2	100	0	58	48	0	0	51	1.00
4562368--4562397	2	15.0	2	100	0	60	0	50	0	50	1.00
4565288--4565384	50	1.9	50	97	0	185	38	9	7	45	1.64
4568278--4568303	5	5.2	5	100	0	52	80	0	0	19	0.71
4569497--4569530	12	2.8	12	90	0	59	32	61	0	5	1.20
4569497--4569530	6	5.7	6	92	0	50	32	61	0	5	1.20
4569667--4569700	6	5.7	6	100	0	68	32	67	0	0	0.91
4569570--4569927	161	2.3	156	84	9	448	25	31	15	26	1.96
4571012--4571675	334	2.0	332	94	2	1158	39	9	4	46	1.56

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