genome.fa.s4.2.7.7.80.10.50.1000.27.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  27  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)
5404915--5404943	3	9.7	3	100	0	58	34	0	0	65	0.93
5405550--5405621	27	2.6	28	82	2	101	40	0	9	50	1.36
5407853--5407897	2	22.5	2	100	0	90	51	0	0	48	1.00
5408065--5408094	12	2.6	12	94	5	53	0	6	0	93	0.35
5411758--5411794	2	18.5	2	100	0	74	51	0	0	48	1.00
5411884--5411915	2	16.0	2	100	0	64	50	0	0	50	1.00
5413463--5413530	28	2.4	27	73	9	64	47	2	7	42	1.46
5415655--5415687	13	2.6	13	95	4	59	57	0	0	42	0.98
5416935--5416985	18	2.8	19	72	19	54	35	1	1	60	1.19
5416985--5417037	26	2.0	27	85	10	74	52	0	1	45	1.11
5417922--5417951	3	10.0	3	100	0	60	33	33	0	33	1.58
5418300--5418330	13	2.3	14	94	5	55	48	0	0	51	1.00
5419819--5419860	12	3.6	12	77	6	50	50	0	0	50	1.00
5420015--5420043	13	2.3	13	94	5	51	62	0	6	31	1.22
5420243--5420277	17	2.0	17	88	5	52	60	0	2	37	1.12
5420551--5420601	19	2.6	21	79	11	56	54	1	0	43	1.11
5429099--5429131	17	2.0	17	88	5	50	51	3	6	39	1.42
5429327--5429385	26	2.2	27	81	3	75	64	0	0	35	0.94
5429361--5429404	18	2.3	19	84	15	63	72	0	0	27	0.85
5429423--5429497	10	7.4	10	72	21	50	61	0	0	38	0.96
5429462--5429520	5	11.4	5	75	20	50	54	1	0	44	1.10
5429934--5429963	10	3.0	10	95	0	51	60	0	3	36	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5430485--5430531	21	2.3	21	85	10	62	34	0	0	65	0.93
5437723--5437799	28	2.6	30	76	17	74	35	2	1	61	1.18
5438368--5438414	21	2.2	21	85	11	60	55	0	0	44	0.99
5441442--5441476	18	1.9	19	88	11	56	34	5	11	48	1.63
5442209--5442250	3	14.0	3	100	0	84	66	0	0	33	0.92
5442342--5442393	14	3.5	14	80	14	59	82	0	17	0	0.66
5442342--5442391	25	2.1	23	85	7	64	84	0	16	0	0.63
5442352--5442392	21	2.0	21	85	9	57	80	0	19	0	0.71
5443378--5443424	14	3.4	14	82	8	60	85	0	12	2	0.70
5443377--5443436	20	3.0	20	76	18	63	81	0	13	5	0.84
5443378--5443435	17	3.4	17	83	7	73	84	0	13	1	0.70
5443379--5443432	14	3.9	13	78	9	54	83	0	14	1	0.73
5443447--5443531	31	2.7	32	86	13	108	32	0	0	67	0.91
5443395--5444287	488	1.8	481	83	8	1176	34	6	9	48	1.62
5444953--5444991	18	2.2	18	86	4	53	33	0	2	64	1.08
5448217--5448242	4	6.5	4	100	0	52	73	0	0	26	0.84
5450644--5450683	2	20.0	2	100	0	80	50	0	0	50	1.00
5458313--5458587	28	9.8	28	77	2	246	26	16	28	28	1.97
5458536--5459110	27	21.0	27	85	3	605	29	13	31	25	1.94
5458536--5459117	164	3.5	162	82	5	634	29	13	31	25	1.94
5458536--5459110	245	2.3	247	84	2	726	29	13	31	25	1.94
5463050--5463911	428	2.0	428	98	0	1661	39	14	23	22	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5465635--5465713	20	3.6	20	69	21	68	39	11	15	34	1.83
5465657--5465710	27	2.0	27	85	0	72	33	12	16	37	1.87
5466761--5466810	16	3.1	17	77	11	61	54	0	0	46	1.00
5466765--5466838	16	4.4	16	75	14	60	56	0	0	43	0.99
5466764--5466838	34	2.2	35	83	11	93	57	0	0	42	0.98
5466779--5466826	20	2.6	19	84	12	57	56	0	0	43	0.99
5466885--5466949	34	1.9	34	87	0	94	52	4	0	43	1.22
5466879--5466950	17	4.2	17	75	10	67	54	4	0	41	1.20
5468094--5468143	20	2.4	22	86	6	68	56	4	4	36	1.37
5468630--5468662	13	2.5	13	90	9	50	27	0	9	63	1.24
5468832--5468866	17	2.1	17	100	0	70	37	0	5	57	1.23
5468836--5468875	17	2.4	17	87	8	55	37	0	7	55	1.29
5468859--5468892	14	2.3	15	95	5	61	38	0	5	55	1.24
5469350--5469393	23	2.0	22	86	13	63	52	4	2	40	1.34
5469346--5469392	12	4.2	11	78	10	51	55	2	2	40	1.24
5471202--5471240	21	1.9	21	89	5	62	53	0	0	46	1.00
5471372--5471407	18	2.0	18	88	0	54	33	5	22	38	1.77
5472977--5473003	2	13.5	2	100	0	54	48	0	0	51	1.00
5476046--5476127	25	3.2	25	83	10	78	53	0	3	42	1.18
5476160--5476211	22	2.3	22	80	3	59	53	5	0	40	1.25
5476222--5476250	15	1.9	15	100	0	58	48	13	0	37	1.43
5476253--5476310	20	3.0	20	82	5	66	55	1	0	43	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5476266--5476314	18	2.8	17	80	17	55	59	2	0	38	1.09
5476266--5476321	16	3.2	17	79	18	62	57	1	0	41	1.09
5477963--5478020	26	2.2	27	78	3	64	60	5	22	12	1.51
5478356--5478390	3	11.7	3	100	0	70	31	0	0	68	0.90
5479839--5480193	50	7.1	50	91	0	523	29	20	19	30	1.97
5482406--5482652	128	1.9	128	94	0	440	37	15	18	28	1.92
5484740--5484809	35	2.0	35	100	0	140	37	20	14	28	1.91
5484775--5484917	50	2.9	50	84	4	189	36	19	12	31	1.89
5485546--5485588	3	14.3	3	95	0	77	65	0	2	32	1.06
5488118--5488167	21	2.3	22	83	13	68	58	0	0	42	0.98
5488118--5488171	12	5.0	11	75	18	51	57	0	0	42	0.98
5488878--5488916	12	3.1	12	82	13	51	41	0	0	58	0.98
5492953--5492982	11	2.8	11	95	5	53	26	0	0	73	0.84
5493723--5493809	43	2.0	43	82	8	106	36	1	4	57	1.27
5495069--5495099	2	15.5	2	100	0	62	48	0	0	51	1.00
5495920--5495954	3	11.7	3	100	0	70	31	0	0	68	0.90
5497300--5497336	19	2.0	19	89	5	58	54	0	0	45	1.00
5497516--5497553	2	19.0	2	100	0	76	50	0	50	0	1.00
5498045--5498084	2	20.5	2	94	5	73	52	0	0	47	1.00
5499702--5499747	22	2.1	21	92	4	74	45	0	2	52	1.13
5499952--5499989	20	1.9	19	89	5	58	47	0	0	52	1.00
5500458--5500507	18	2.7	18	82	17	59	68	2	0	30	1.01
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5500441--5500507	24	2.7	24	84	9	73	67	1	0	31	1.00
5500445--5500499	29	1.9	28	85	3	74	69	1	0	29	0.99
5501477--5501546	19	3.8	19	76	14	58	50	1	2	45	1.25
5501903--5501946	22	2.0	22	82	8	54	52	6	0	40	1.28
5503939--5503969	2	15.5	2	100	0	62	48	0	0	51	1.00
5506233--5506518	13	21.8	13	74	8	188	26	18	25	29	1.98
5506353--5506405	25	2.1	26	82	10	65	28	15	20	35	1.93
5506351--5506419	14	5.2	14	75	15	58	26	15	21	36	1.94
5506396--5506510	40	2.9	40	80	7	117	30	20	22	26	1.98
5506388--5506512	27	4.7	27	77	5	119	28	19	22	29	1.98
5509020--5509585	67	8.4	67	83	4	655	24	20	18	36	1.95
5509020--5509585	134	4.2	134	85	1	724	24	20	18	36	1.95
5509070--5509585	201	2.6	201	89	0	771	24	20	18	36	1.95
5509017--5509623	201	3.0	200	83	3	731	24	21	17	36	1.95
5510101--5510519	13	32.2	13	74	6	285	26	19	26	27	1.99
5510101--5510519	25	16.1	26	74	6	285	26	19	26	27	1.99
5510101--5510490	38	10.0	38	72	7	225	26	20	26	26	1.99
5510253--5510348	27	3.6	27	71	5	95	25	19	22	32	1.98
5510337--5510428	27	3.5	27	79	5	98	30	21	21	26	1.99
5514510--5514554	16	2.8	16	83	12	56	57	2	2	37	1.23
5515731--5515781	16	3.2	16	74	20	52	56	9	0	33	1.32
5522362--5522404	19	2.3	19	84	8	52	41	0	0	58	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5525106--5525173	33	2.0	34	85	2	93	19	2	27	50	1.62
5527726--5527811	42	2.0	43	88	2	129	43	9	12	34	1.75
5528218--5528256	16	2.4	16	91	0	60	74	0	0	25	0.82
5528976--5529016	18	2.3	18	87	4	57	56	0	2	41	1.13
5529285--5529320	14	2.6	14	86	13	56	50	0	0	50	1.00
5532178--5532242	18	3.5	18	73	12	60	53	1	3	41	1.25
5532533--5532575	16	2.6	17	82	10	54	55	2	0	41	1.12
5532793--5532827	11	3.1	11	91	4	52	57	11	8	22	1.61
5533244--5533276	16	2.0	17	94	5	59	27	0	0	72	0.85
5533244--5533281	8	4.3	9	81	18	53	31	0	0	68	0.90

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