genome.fa.s48.2.7.7.80.10.50.1000.25.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: Scaffold48
Parameters: 2 7 7 80 10 50 1000
Length:  4619657

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   

This is table  25  of  27  ( 3212 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)
3940886--3940931	21	2.0	23	84	12	60	67	4	0	28	1.10
3941836--3941946	56	1.9	58	87	7	165	49	5	10	34	1.61
3942688--3942727	15	2.5	15	88	8	53	0	17	2	80	0.83
3942686--3942745	19	3.0	20	83	13	72	1	20	1	76	0.96
3943213--3943281	27	2.5	26	77	9	75	68	8	1	21	1.25
3944724--3944802	39	2.0	39	97	0	149	35	20	15	29	1.93
3945227--3945256	2	15.0	2	100	0	60	50	0	0	50	1.00
3945721--3945787	16	4.1	15	75	17	53	44	0	1	53	1.09
3945732--3945787	17	3.4	17	77	20	64	42	0	1	55	1.10
3962002--3962059	5	11.4	5	74	22	50	39	0	0	60	0.97
3962001--3962054	15	3.5	15	77	22	58	40	0	0	59	0.98
3962008--3962059	9	5.8	9	78	17	63	40	0	0	59	0.97
3966711--3966738	2	14.0	2	100	0	56	50	0	0	50	1.00
3967118--3967154	15	2.3	17	90	9	60	48	0	2	48	1.15
3971506--3971536	2	15.5	2	100	0	62	48	0	0	51	1.00
3976163--3976189	3	9.0	3	100	0	54	33	0	0	66	0.92
3977851--3977904	27	2.0	26	86	10	74	35	1	1	61	1.18
3986255--3986338	40	2.1	40	91	4	134	44	3	7	45	1.48
3986724--3986767	2	22.0	2	100	0	88	50	0	0	50	1.00
3987003--3987051	18	2.7	18	84	9	64	14	2	4	79	0.97
3989893--3989918	2	13.0	2	100	0	52	50	0	0	50	1.00
3991211--3991240	2	15.0	2	100	0	60	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3991161--3991275	61	1.9	60	98	1	221	38	12	5	44	1.64
3991537--3991569	2	16.5	2	100	0	66	48	0	0	51	1.00
3996374--3996433	26	2.3	27	80	11	70	48	1	3	46	1.28
3996607--3996641	6	5.8	6	96	0	52	40	0	8	51	1.33
3997716--3997755	2	20.5	2	94	5	73	50	0	0	50	1.00
3997865--3997909	23	2.0	23	86	4	65	44	0	0	55	0.99
3997891--3997919	10	3.0	10	95	5	51	31	0	0	68	0.89
3997867--3997989	18	7.0	17	67	21	58	38	1	0	59	1.13
3998375--3998433	5	12.4	5	77	16	54	55	1	0	42	1.09
3998365--3998428	29	2.2	28	86	5	83	57	1	0	40	1.08
3998385--3998437	18	2.8	18	88	5	70	52	0	0	47	1.00
3998374--3998430	14	4.1	14	80	6	62	54	1	0	43	1.10
3998412--3998488	31	3.0	24	72	24	66	40	0	0	59	0.97
3998412--3998488	6	12.8	6	72	20	63	40	0	0	59	0.97
3998436--3998497	17	3.8	16	76	18	56	43	0	0	56	0.99
3998404--3998496	42	2.2	40	78	19	109	44	0	0	55	0.99
4003355--4003476	59	2.1	59	88	0	181	31	13	16	39	1.87
4012057--4012083	12	2.2	12	100	0	54	77	0	7	14	0.97
4016558--4016586	11	2.5	12	88	11	51	31	0	0	68	0.89
4027170--4027196	2	13.5	2	100	0	54	51	0	0	48	1.00
4029030--4029058	3	9.7	3	100	0	58	34	65	0	0	0.93
4029373--4029399	2	13.5	2	100	0	54	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4030270--4030327	17	3.2	17	76	11	53	39	0	0	60	0.97
4030274--4030318	21	2.2	20	84	4	54	37	0	0	62	0.96
4032272--4032317	23	2.0	22	87	4	65	50	2	0	47	1.13
4034112--4034139	2	14.0	2	100	0	56	50	0	0	50	1.00
4034366--4034393	2	14.0	2	100	0	56	0	50	0	50	1.00
4036444--4036473	2	15.0	2	100	0	60	50	0	50	0	1.00
4036874--4036906	3	11.0	3	100	0	66	0	33	0	66	0.92
4037791--4037820	2	15.0	2	100	0	60	50	0	50	0	1.00
4060073--4060103	2	15.5	2	100	0	62	51	0	0	48	1.00
4060891--4060969	28	2.9	27	81	7	81	59	0	0	40	0.97
4060891--4060935	15	2.8	16	83	13	56	60	0	0	40	0.97
4060915--4060994	27	2.9	27	78	14	83	57	0	2	40	1.12
4061637--4061676	19	2.0	21	85	9	57	57	0	0	42	0.98
4062374--4062416	19	2.3	19	84	11	61	37	0	2	60	1.10
4063496--4063532	14	2.6	14	86	0	56	29	8	0	62	1.24
4067003--4067066	24	2.7	24	76	23	64	53	0	1	45	1.10
4067036--4067071	17	2.1	17	89	0	54	55	0	2	41	1.14
4068443--4068473	14	2.1	15	94	5	55	80	0	19	0	0.71
4073351--4073382	2	16.0	2	100	0	64	50	0	0	50	1.00
4074108--4074317	109	1.9	109	95	1	377	36	18	9	36	1.82
4074341--4074392	14	3.6	14	82	7	59	57	0	0	42	0.98
4080172--4080378	102	2.0	102	91	0	333	23	31	19	25	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4082368--4082409	16	2.6	16	88	3	57	45	0	2	52	1.13
4082380--4082452	25	3.0	24	75	11	76	46	0	0	53	1.00
4082846--4082895	25	2.0	24	88	3	73	56	2	0	42	1.11
4083847--4083903	18	3.2	18	73	24	57	42	0	0	57	0.98
4087676--4087706	15	2.1	15	93	0	53	51	3	0	45	1.17
4088127--4088206	18	4.7	18	76	14	71	61	1	1	36	1.12
4088163--4088206	16	2.8	16	80	13	54	61	0	0	38	0.96
4088146--4088270	39	3.2	39	75	17	125	60	0	0	38	1.08
4088154--4088272	20	6.3	18	73	19	82	59	0	0	38	1.09
4088320--4088368	7	7.3	7	80	13	50	16	0	12	71	1.14
4088320--4088368	13	3.6	14	76	18	50	16	0	12	71	1.14
4088920--4088974	15	3.7	14	81	11	65	36	0	0	63	0.95
4088938--4088978	20	2.0	20	90	0	64	43	0	0	56	0.99
4089126--4089168	3	14.7	3	90	4	70	32	0	0	67	0.91
4098908--4098995	39	2.2	39	80	11	99	40	6	6	45	1.57
4098991--4099028	2	19.0	2	100	0	76	50	0	0	50	1.00
4099521--4099553	3	11.0	3	100	0	66	33	0	0	66	0.92
4099997--4100040	17	2.5	17	88	7	61	38	0	6	54	1.27
4102648--4102678	2	15.5	2	100	0	62	0	48	0	51	1.00
4107036--4107060	2	12.5	2	100	0	50	52	0	0	48	1.00
4107971--4108001	3	10.7	3	93	6	55	64	0	0	35	0.94
4108000--4108029	3	10.3	3	92	7	53	33	0	0	66	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4108069--4108097	2	14.5	2	100	0	58	51	0	0	48	1.00
4109492--4109521	2	15.0	2	100	0	60	50	0	0	50	1.00
4117147--4117190	2	22.0	2	100	0	88	50	0	0	50	1.00
4117246--4117292	16	3.0	15	82	11	58	0	2	12	85	0.70
4119732--4119823	46	2.0	46	95	0	166	28	19	17	34	1.94
4121934--4122032	2	49.5	2	88	0	117	49	6	2	42	1.39
4123445--4123491	23	2.0	23	83	0	58	55	2	0	42	1.12
4124521--4124714	99	2.0	99	96	0	361	33	5	11	48	1.63
4130010--4130038	14	2.1	14	100	0	58	41	0	58	0	0.98
4141251--4141283	2	16.5	2	100	0	66	48	0	0	51	1.00
4143655--4143690	2	18.0	2	100	0	72	50	0	0	50	1.00
4145649--4145682	10	3.8	9	88	11	52	79	0	0	20	0.73
4155295--4155336	22	2.0	21	85	4	57	50	9	4	35	1.56
4155948--4156011	29	2.2	30	81	13	71	53	1	0	45	1.10
4162105--4162160	20	3.0	18	78	19	53	42	1	3	51	1.29
4162509--4162579	30	2.5	28	80	14	83	50	0	4	45	1.21
4162522--4162579	30	2.0	29	89	3	89	50	0	3	46	1.18
4163696--4163724	2	14.5	2	100	0	58	48	0	0	51	1.00
4164210--4164248	13	3.1	12	82	10	51	38	0	2	58	1.12
4166707--4166753	19	2.7	17	81	12	51	63	4	2	29	1.25
4168356--4168403	23	2.0	23	84	4	60	37	12	12	37	1.81
4173204--4173231	13	2.2	13	100	0	56	32	25	7	35	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4180705--4180763	29	2.0	31	84	15	81	45	1	0	52	1.10
4185915--4185976	27	2.3	27	77	5	72	46	1	1	50	1.20
4196048--4196086	3	13.0	3	100	0	78	66	0	0	33	0.92
4197478--4197505	2	14.0	2	100	0	56	50	0	0	50	1.00
4202379--4202420	21	2.0	21	86	9	59	69	0	0	30	0.89
4202381--4202420	20	2.0	20	85	5	53	70	0	0	30	0.88
4202395--4202464	20	3.4	19	69	16	50	58	1	0	40	1.07
4208927--4208971	2	22.5	2	95	0	81	48	0	48	2	1.13
4209585--4209643	29	2.0	29	96	0	109	42	11	10	35	1.76
4225631--4225706	30	2.6	28	77	6	80	53	0	0	46	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