genome.fa.s11.2.7.7.80.10.50.1000.24.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: Scaffold11
Parameters: 2 7 7 80 10 50 1000
Length:  5230303

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   

This is table  24  of  29  ( 3461 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)
3906443--3906484	22	1.9	22	85	0	57	40	0	7	52	1.29
3906473--3906523	15	3.2	16	76	18	54	52	1	0	45	1.12
3906518--3906571	27	2.0	27	82	10	65	53	9	0	37	1.33
3906637--3906677	20	2.0	20	86	9	57	26	7	0	65	1.18
3907982--3908035	21	2.5	22	79	14	67	42	0	0	57	0.98
3908208--3908245	19	2.0	19	85	10	51	57	0	0	42	0.98
3909934--3909967	16	2.1	17	88	5	52	61	0	0	38	0.96
3909980--3910018	20	2.0	20	90	10	62	48	0	0	51	1.00
3910782--3910847	31	2.1	32	85	2	89	43	0	0	56	0.99
3910940--3911786	422	2.0	422	94	0	1480	22	23	24	29	1.99
3915649--3915679	2	15.5	2	100	0	62	48	0	0	51	1.00
3915703--3915729	2	13.5	2	100	0	54	48	0	0	51	1.00
3915827--3915852	2	13.0	2	100	0	52	50	0	0	50	1.00
3919881--3919923	3	14.7	3	85	4	61	30	0	4	65	1.13
3931930--3931993	30	2.1	30	100	0	128	43	20	17	18	1.88
3936291--3936330	18	2.3	17	82	4	53	15	10	5	70	1.32
3936422--3936470	19	2.5	19	81	12	64	48	0	2	48	1.12
3936427--3936464	20	1.9	20	89	10	60	42	0	2	55	1.14
3942282--3942375	27	3.5	27	82	8	104	48	5	0	45	1.25
3943555--3943595	12	3.5	12	93	6	75	36	0	0	63	0.95
3943589--3943674	20	4.3	20	64	29	58	45	1	0	53	1.07
3943587--3943689	31	3.4	31	79	14	133	43	0	0	55	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3943601--3943687	14	5.9	14	67	20	52	45	1	0	52	1.08
3944659--3944697	2	19.5	2	100	0	78	0	48	0	51	1.00
3944697--3944721	2	12.5	2	100	0	50	48	0	0	52	1.00
3944905--3944967	3	22.7	3	73	23	50	69	1	0	28	0.97
3944908--3944964	11	5.1	10	76	17	51	70	1	0	28	0.98
3944964--3945052	32	2.7	33	82	10	110	55	0	0	44	0.99
3944969--3945023	16	3.4	16	72	20	51	54	0	0	45	0.99
3944973--3945060	20	4.8	19	74	24	66	53	0	0	46	1.00
3945270--3945327	31	1.9	30	86	10	82	51	3	0	44	1.18
3945650--3945728	27	3.0	27	76	10	74	46	1	1	50	1.17
3945716--3945794	24	3.3	24	75	8	65	55	0	0	44	0.99
3945753--3945794	22	2.0	21	90	4	66	61	0	0	38	0.96
3946248--3946301	22	2.5	21	77	11	56	46	3	5	44	1.44
3946733--3946769	2	18.5	2	94	0	65	51	2	0	45	1.15
3947427--3947491	30	2.2	30	83	8	80	50	1	0	47	1.10
3948396--3948432	16	2.3	16	90	0	56	64	0	0	35	0.94
3948471--3948513	22	2.0	21	86	13	61	55	2	0	41	1.12
3950020--3950045	2	13.0	2	100	0	52	50	0	0	50	1.00
3951962--3951996	16	2.2	16	89	0	52	74	0	0	25	0.82
3952034--3952075	22	2.0	21	86	9	59	57	0	0	42	0.99
3952143--3952198	27	2.0	28	93	3	96	55	0	0	44	0.99
3952162--3952202	16	2.5	16	88	4	55	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)
3952217--3952306	31	2.9	31	77	9	94	58	2	0	38	1.10
3952181--3952306	31	3.9	31	76	15	87	57	3	0	38	1.14
3960339--3960367	3	9.7	3	100	0	58	0	31	0	68	0.89
3964680--3964714	15	2.3	15	100	0	70	37	0	40	22	1.55
3966825--3966856	7	4.6	7	92	0	55	90	9	0	0	0.45
3968597--3968622	2	13.0	2	100	0	52	50	0	0	50	1.00
3969133--3969159	2	13.5	2	100	0	54	51	0	48	0	1.00
3976330--3976369	20	2.0	21	85	14	57	45	5	2	47	1.38
3977314--3977352	19	2.1	19	85	9	53	61	0	0	38	0.96
3977313--3977353	20	2.0	20	85	4	55	60	0	0	39	0.96
3978594--3978630	20	1.9	19	89	10	58	48	0	0	51	1.00
3984326--3984362	2	18.5	2	100	0	74	51	0	0	48	1.00
3990336--3990554	34	6.5	34	83	2	253	26	6	25	42	1.79
3990340--3990554	102	2.1	101	86	1	295	26	6	25	41	1.79
3991253--3991317	17	3.8	17	70	10	51	50	1	4	43	1.32
3991569--3991608	21	1.9	21	94	0	71	47	5	22	25	1.71
3993066--3993098	2	16.5	2	100	0	66	51	0	48	0	1.00
3997117--3997241	66	1.9	66	84	0	169	44	12	6	36	1.67
4014343--4014378	15	2.4	15	90	0	54	52	0	0	47	1.00
4014724--4014787	16	3.9	16	78	13	76	56	0	0	43	0.99
4014727--4014810	16	5.1	16	74	16	73	58	0	0	41	0.98
4014734--4014796	18	3.4	18	72	16	58	57	0	0	42	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4014746--4014829	25	3.3	25	76	15	66	59	0	0	40	0.97
4014930--4014975	18	2.6	17	73	26	51	45	2	0	52	1.13
4017087--4017147	24	2.7	23	76	16	63	42	1	0	55	1.09
4017095--4017159	16	4.2	15	75	18	62	43	1	0	55	1.09
4017166--4017205	13	3.1	13	85	0	53	27	2	0	70	1.01
4017284--4017320	2	18.5	2	94	0	65	54	0	45	0	1.00
4017682--4017728	24	2.0	24	83	8	60	63	4	0	31	1.13
4018226--4018268	21	2.2	19	84	16	52	58	0	2	39	1.11
4019019--4019044	4	6.5	4	100	0	52	76	0	0	23	0.78
4036937--4037032	25	3.7	25	76	16	88	54	1	1	43	1.14
4036985--4037326	124	2.8	125	84	10	413	55	1	2	40	1.22
4037613--4037687	23	3.2	23	74	12	73	30	1	5	62	1.25
4037613--4037704	47	1.9	48	82	10	118	35	1	4	58	1.25
4037626--4037722	47	2.1	47	80	7	108	36	3	3	57	1.30
4037662--4037940	118	2.4	113	84	8	345	41	2	2	53	1.27
4037857--4037912	25	2.2	26	78	15	64	41	0	0	58	0.98
4037921--4037985	30	2.2	29	83	8	87	46	0	0	53	1.00
4038350--4038390	20	2.0	21	90	4	66	53	0	0	46	1.00
4043819--4043847	3	9.7	3	100	0	58	68	0	0	31	0.89
4046258--4046301	21	2.2	20	84	8	54	52	0	0	47	1.00
4046281--4046322	17	2.8	15	86	13	52	52	0	0	47	1.00
4053191--4053243	27	2.0	25	82	13	63	50	1	1	45	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4054084--4054133	17	2.9	17	78	3	55	54	8	2	36	1.42
4055471--4055507	2	18.5	2	100	0	74	48	0	0	51	1.00
4069893--4069917	11	2.3	11	100	0	50	48	0	8	44	1.32
4070648--4070712	27	2.4	27	81	2	76	29	4	20	46	1.70
4081124--4081165	3	14.0	3	94	0	75	30	0	2	66	1.04
4081216--4081249	16	2.1	16	100	0	68	47	20	8	23	1.78
4113906--4113934	2	14.5	2	100	0	58	48	0	0	51	1.00
4119333--4119592	50	5.2	50	86	3	371	33	21	17	27	1.96
4119333--4119592	100	2.6	100	91	1	423	33	21	17	27	1.96
4119814--4120076	130	2.0	130	96	0	481	28	20	15	34	1.94
4123354--4123378	13	1.9	13	100	0	50	36	16	16	32	1.90
4123442--4123466	13	1.9	13	100	0	50	32	16	16	36	1.90
4123475--4123599	52	2.4	52	94	0	214	36	17	17	28	1.93
4131775--4131856	30	2.7	31	86	7	114	26	30	18	24	1.98
4131836--4132779	34	28.0	34	84	7	1072	21	32	11	34	1.89
4131834--4132779	207	4.7	206	85	5	1147	21	32	11	34	1.89
4131841--4132779	241	4.0	240	86	5	1126	21	32	11	34	1.89
4132593--4132773	33	6.0	28	73	16	107	23	32	13	30	1.93
4132654--4132767	60	1.9	60	85	7	160	25	33	14	27	1.94
4132784--4132913	32	4.1	32	92	3	219	28	37	17	16	1.91
4132784--4132906	65	1.9	66	96	1	230	27	37	17	17	1.92
4132906--4133344	49	8.9	49	90	1	628	25	26	17	31	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4132906--4133335	146	2.9	147	93	1	691	25	26	17	31	1.97
4134254--4134320	33	2.0	33	88	0	98	34	11	13	40	1.81
4134274--4134298	13	1.9	13	100	0	50	36	16	16	32	1.90
4134363--4134387	13	1.9	13	100	0	50	32	16	16	36	1.90
4134396--4134520	52	2.4	52	95	0	223	36	18	17	28	1.94
4138336--4138378	19	2.3	19	91	0	68	37	18	18	25	1.94
4138631--4138840	50	4.2	50	86	3	289	31	20	20	28	1.97
4139081--4139119	3	13.0	3	100	0	78	33	0	0	66	0.92
4142965--4143002	2	19.0	2	94	0	67	50	2	0	47	1.15
4145593--4145638	14	3.4	14	82	5	51	52	0	0	47	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   28   29