genome.fa.s71.2.7.7.80.10.50.1000.29.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: Scaffold71
Parameters: 2 7 7 80 10 50 1000
Length:  5741892

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  29  of  33  ( 3929 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)
4928995--4929292	165	1.8	163	87	4	447	38	2	1	57	1.22
4929228--4929304	23	3.2	24	76	12	77	36	3	0	59	1.16
4929250--4929296	11	4.2	11	84	10	60	29	2	0	68	1.02
4929243--4929297	12	4.7	12	79	18	62	32	1	0	65	1.03
4929243--4929305	11	5.2	13	76	17	57	33	3	0	63	1.10
4932026--4932320	141	2.1	141	92	0	482	27	43	10	18	1.83
4932308--4932378	30	2.4	30	92	0	115	36	39	15	8	1.78
4932167--4932534	204	1.8	201	89	1	574	30	41	12	16	1.85
4934870--4934902	2	16.5	2	93	0	57	0	3	45	51	1.16
4935908--4935942	18	1.9	18	94	0	61	54	0	2	42	1.15
4942657--4942690	2	17.0	2	87	0	50	0	44	0	55	0.99
4942657--4942690	12	2.8	12	95	0	59	0	44	0	55	0.99
4948453--4948498	24	1.9	24	83	16	60	36	0	4	58	1.18
4948628--4948674	16	2.9	16	79	17	53	51	0	0	48	1.00
4949212--4949301	41	2.2	40	96	2	162	40	10	0	50	1.36
4949443--4949477	11	3.1	11	88	8	52	31	0	0	68	0.90
4949443--4949477	12	3.0	12	91	4	54	31	0	0	68	0.90
4950084--4950113	13	2.2	14	94	5	53	33	0	0	66	0.92
4952708--4952742	2	17.5	2	100	0	70	48	0	0	51	1.00
4965771--4965823	23	2.3	23	80	6	63	41	5	0	52	1.25
4965885--4965924	5	8.2	5	91	5	55	55	0	5	40	1.22
4967251--4967285	2	17.5	2	100	0	70	51	0	48	0	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4971164--4971207	23	1.9	23	90	0	70	52	2	40	4	1.34
4971865--4971916	11	4.3	12	77	15	54	30	0	0	69	0.89
4971864--4971895	16	2.0	16	93	0	55	34	0	0	65	0.93
4971869--4971919	19	2.9	17	78	13	59	29	0	0	70	0.87
4972793--4972833	13	3.4	13	77	19	52	39	0	0	60	0.96
4972909--4972968	23	2.8	20	79	18	66	30	0	3	66	1.07
4972953--4972990	5	7.8	5	83	16	53	42	0	0	57	0.98
4972907--4972968	22	2.9	21	79	13	72	29	0	3	67	1.06
4972953--4972992	13	3.4	11	83	16	53	42	0	0	57	0.98
4972955--4972991	18	2.0	19	94	5	67	43	0	0	56	0.99
4974077--4974137	17	3.7	16	72	14	61	31	1	0	67	1.01
4974054--4974133	8	10.0	8	85	5	90	31	1	0	67	0.99
4974107--4974174	37	1.9	36	85	11	97	35	2	0	61	1.11
4980215--4980248	16	2.1	17	88	5	52	55	0	5	38	1.24
4982322--4982351	2	15.0	2	100	0	60	50	0	0	50	1.00
4984723--4984758	2	18.5	2	88	5	56	52	0	47	0	1.00
4987033--4987057	6	4.2	6	100	0	50	68	0	0	32	0.90
4987576--4987616	2	20.5	2	100	0	82	48	0	0	51	1.00
4989943--4989969	4	6.8	4	100	0	54	51	22	0	25	1.48
4990869--4990899	2	15.5	2	100	0	62	51	0	0	48	1.00
4992337--4992429	29	3.3	28	72	14	84	40	2	0	56	1.11
4993284--4993343	23	2.9	22	76	14	65	60	0	0	40	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4993315--4993350	14	2.5	15	91	8	58	66	0	0	33	0.92
4993286--4993343	18	2.9	18	75	22	53	62	0	0	37	0.96
4995750--4995779	10	3.0	10	95	0	51	50	3	0	46	1.18
4995892--4995951	21	2.8	21	80	19	79	50	1	0	48	1.11
4996940--4996985	2	23.0	2	100	0	92	50	0	50	0	1.00
4997229--4997254	2	13.0	2	100	0	52	50	0	0	50	1.00
5011912--5012020	53	2.1	50	88	11	157	54	1	3	40	1.29
5013087--5013151	33	2.0	33	100	0	130	41	3	0	55	1.15
5018457--5018507	26	1.9	27	88	4	77	35	1	0	62	1.06
5019332--5019367	7	5.4	7	87	12	58	38	0	0	61	0.96
5019312--5019367	12	4.5	12	79	14	51	39	0	0	60	0.97
5019332--5019410	14	5.7	13	74	16	61	39	0	2	58	1.12
5019320--5019367	19	2.5	18	83	12	60	39	0	0	60	0.97
5019306--5019422	56	2.1	58	82	12	145	38	0	1	59	1.07
5019831--5019871	13	3.1	14	83	13	52	39	0	0	60	0.96
5019805--5019873	16	4.2	17	70	25	51	40	0	0	59	0.97
5019802--5019865	8	8.4	8	76	20	50	39	0	0	60	0.97
5020375--5020399	13	1.9	13	100	0	50	64	0	0	36	0.94
5020689--5020734	6	7.7	6	81	18	60	34	0	0	65	0.93
5020688--5020734	11	4.6	11	77	17	57	34	0	0	65	0.93
5020689--5020734	19	2.6	17	93	6	74	34	0	0	65	0.93
5020698--5020746	24	2.0	24	84	7	64	36	4	0	59	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5020689--5020748	19	3.2	19	86	9	70	36	3	0	60	1.14
5020866--5020914	23	2.0	25	84	11	66	53	0	0	46	1.00
5020878--5020961	27	3.0	27	68	16	64	55	1	0	42	1.07
5021482--5021525	21	2.2	19	84	8	52	65	2	0	31	1.05
5022140--5022218	25	3.3	23	70	20	63	37	0	0	62	0.96
5022136--5022200	29	2.4	26	87	10	94	35	0	0	64	0.94
5022193--5022235	18	2.4	18	80	0	50	37	0	2	60	1.10
5022803--5022832	6	5.2	6	92	8	53	53	0	0	46	1.00
5022803--5022832	11	2.6	12	94	5	53	53	0	0	46	1.00
5023001--5023066	32	2.1	32	82	5	80	51	0	0	48	1.00
5023040--5023082	20	2.0	21	86	13	61	51	0	0	48	1.00
5023077--5023119	20	2.2	20	87	4	61	58	2	0	39	1.11
5023077--5023135	20	3.0	18	80	14	55	59	1	0	38	1.08
5023373--5023398	2	13.0	2	100	0	52	0	0	50	50	1.00
5023793--5023839	22	2.1	23	84	11	62	40	0	2	57	1.11
5025165--5025246	32	2.5	33	76	15	89	56	0	1	42	1.07
5025186--5025253	31	2.2	31	87	10	95	54	0	1	44	1.09
5025186--5025264	31	2.5	32	84	8	92	53	0	2	44	1.14
5026489--5026604	58	2.0	58	98	0	223	39	15	11	33	1.83
5031582--5031629	21	2.3	22	82	7	55	47	2	0	50	1.12
5031618--5031652	18	2.0	18	88	5	54	34	0	0	65	0.93
5032164--5032240	28	2.9	27	79	11	77	37	0	2	59	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5032147--5032237	17	4.9	19	72	14	75	40	0	2	57	1.11
5032158--5032239	26	3.0	26	73	18	78	39	0	2	58	1.11
5032192--5032261	28	2.5	28	84	11	81	35	1	1	61	1.14
5032192--5032261	27	2.5	28	86	6	81	35	1	1	61	1.14
5033305--5033347	21	2.0	21	82	8	52	55	0	0	44	0.99
5033909--5033935	3	9.0	3	100	0	54	66	0	0	33	0.92
5035767--5035851	20	4.4	20	71	16	72	42	1	0	56	1.07
5035767--5035829	18	3.4	18	71	20	58	46	1	0	52	1.10
5035817--5035860	23	2.0	23	90	4	72	34	0	0	65	0.93
5035717--5035860	11	12.4	12	68	24	62	39	1	0	59	1.06
5036182--5036221	6	6.5	6	82	5	53	2	30	2	65	1.19
5037610--5037654	18	2.4	20	82	14	60	33	0	0	66	0.92
5038823--5038972	80	1.9	82	90	2	241	48	8	2	41	1.47
5040447--5040475	2	14.5	2	100	0	58	48	0	0	51	1.00
5042345--5042387	19	2.3	19	88	8	61	27	0	2	69	1.00
5043104--5043142	18	2.2	18	86	9	53	61	0	0	38	0.96
5044458--5044510	27	2.0	27	96	0	97	39	5	24	30	1.78
5049514--5049934	207	2.0	207	99	0	833	21	20	18	39	1.93
5051833--5051871	17	2.1	17	86	13	51	43	0	0	56	0.99
5051827--5051879	19	2.8	18	76	21	54	43	0	1	54	1.11
5058938--5058985	6	8.0	6	80	0	60	52	2	2	43	1.24
5058938--5058991	18	3.0	18	80	0	63	55	1	1	40	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5059140--5059194	25	2.3	24	82	14	69	49	0	0	50	1.00
5062532--5062557	2	13.0	2	100	0	52	50	0	0	50	1.00
5062769--5062841	23	3.0	25	78	9	80	56	0	1	42	1.08
5063388--5063430	22	1.9	23	90	4	70	58	0	0	41	0.98
5065330--5065371	22	2.0	20	82	17	50	38	7	0	54	1.28
5066816--5066840	2	12.5	2	100	0	50	52	0	48	0	1.00
5066862--5066899	4	9.5	4	100	0	76	73	0	26	0	0.83
5068841--5068905	18	3.9	16	72	27	55	52	1	0	46	1.10
5068831--5068906	30	2.5	31	81	14	86	55	1	0	43	1.08
5074338--5074365	14	2.0	14	100	0	56	28	28	0	42	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   32   
          33