genome.fa.s258.2.7.7.80.10.50.1000.19.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: Scaffold258
Parameters: 2 7 7 80 10 50 1000
Length:  5730937

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   

This is table  19  of  25  ( 2900 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)
4534943--4534980	18	2.1	18	100	0	76	21	34	7	36	1.82
4537869--4537902	5	6.8	5	89	0	50	47	0	52	0	1.00
4539444--4539489	2	24.5	2	85	12	62	45	2	0	52	1.13
4541367--4541404	16	2.4	16	86	8	51	60	0	5	34	1.19
4541362--4541404	16	2.7	15	85	10	50	55	0	6	37	1.27
4543014--4543076	21	3.0	21	79	9	74	53	3	0	42	1.16
4543012--4543060	12	4.5	11	80	14	57	57	0	0	42	0.99
4543163--4543203	21	1.9	22	90	5	66	51	7	0	41	1.30
4543418--4543503	38	2.3	38	83	4	102	34	6	22	36	1.81
4548055--4548173	38	3.1	37	84	7	134	29	10	28	31	1.90
4548883--4548943	23	2.6	25	78	17	69	39	0	0	60	0.97
4548896--4548946	17	3.0	17	85	0	66	33	0	0	66	0.92
4549948--4549981	2	17.0	2	100	0	68	50	0	0	50	1.00
4550187--4550247	15	3.8	16	69	14	54	54	3	0	42	1.17
4550177--4550249	33	2.3	33	76	11	80	52	2	0	45	1.15
4550705--4550814	12	10.0	11	67	21	70	49	0	0	50	1.07
4550763--4550814	17	3.1	16	81	8	59	46	1	0	51	1.12
4550705--4550816	6	19.2	6	69	20	51	49	0	0	50	1.06
4553165--4553206	22	1.9	23	85	9	61	38	0	2	59	1.10
4553343--4553376	15	2.2	15	89	5	50	38	0	0	61	0.96
4553970--4554005	19	1.9	18	88	5	54	52	0	8	38	1.32
4556658--4556728	28	2.5	30	77	15	78	47	1	1	49	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4558990--4559053	32	2.0	32	100	0	128	25	3	31	40	1.71
4559074--4559113	18	2.2	18	100	0	80	17	20	15	47	1.83
4559444--4560436	492	2.0	492	87	3	1449	43	8	6	41	1.61
4561189--4561226	3	12.7	3	100	0	76	65	0	0	34	0.93
4561361--4561424	27	2.4	28	78	7	78	39	1	1	57	1.17
4561434--4561543	9	10.8	9	72	22	69	50	1	0	47	1.18
4561417--4561541	21	5.9	20	74	16	94	51	1	0	46	1.16
4561456--4561515	31	2.0	31	83	9	79	45	3	1	50	1.28
4561433--4561542	11	10.6	10	70	18	73	50	1	0	47	1.18
4561442--4561543	31	3.3	31	70	20	70	49	1	0	48	1.19
4561472--4561616	21	7.0	21	70	7	109	48	2	2	46	1.28
4561958--4562039	43	1.9	42	82	9	103	37	1	3	57	1.24
4562053--4562090	17	2.2	17	86	9	51	28	0	2	68	1.03
4563267--4563334	16	4.2	16	70	26	54	52	1	0	45	1.09
4563245--4563332	33	2.7	33	76	8	92	53	1	0	45	1.07
4563373--4563527	77	2.0	77	92	0	256	25	10	22	41	1.85
4563640--4563667	2	14.0	2	100	0	56	50	0	50	0	1.00
4563911--4563961	24	2.1	24	82	7	59	56	0	0	43	0.99
4570388--4570445	26	2.3	24	82	14	64	46	0	1	51	1.11
4570382--4570452	28	2.5	30	77	15	78	47	0	1	50	1.09
4572995--4573026	2	16.0	2	100	0	64	50	0	0	50	1.00
4573207--4573248	16	2.7	16	85	10	52	50	2	0	47	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4575701--4575836	2	77.0	2	71	23	101	54	1	1	42	1.18
4575701--4575834	20	6.9	20	75	16	124	54	1	1	42	1.18
4575701--4575841	25	5.9	24	77	14	141	55	1	1	41	1.17
4575702--4575842	70	2.0	73	84	9	193	56	1	1	41	1.17
4575882--4575907	7	3.7	7	100	0	52	15	0	0	84	0.62
4580451--4580485	17	2.1	17	100	0	70	17	11	28	42	1.83
4580468--4580928	89	5.2	88	80	5	412	37	14	16	31	1.89
4580468--4580949	176	2.7	175	83	3	563	38	14	16	30	1.88
4580468--4580951	265	1.8	264	82	3	614	38	14	16	30	1.89
4580965--4581004	15	2.9	14	86	13	57	67	0	5	27	1.11
4582318--4582350	13	2.4	14	85	10	50	51	3	6	39	1.42
4584926--4584988	31	2.0	31	93	0	108	20	30	7	41	1.81
4585721--4585817	21	4.5	21	71	14	58	49	4	3	43	1.37
4585795--4585892	42	2.3	42	84	3	117	47	6	5	40	1.50
4585795--4585861	21	3.2	21	80	0	80	53	7	1	37	1.38
4589445--4589538	1	94.0	1	78	0	80	0	7	5	87	0.68
4589448--4589537	33	2.8	33	94	5	157	0	7	5	86	0.70
4597589--4597617	12	2.3	13	94	5	51	75	6	6	10	1.17
4597738--4597821	30	3.3	24	67	25	57	52	0	1	46	1.08
4598517--4598557	1	41.0	1	85	0	55	0	0	7	92	0.38
4598504--4598545	19	2.3	19	87	4	59	0	4	11	83	0.79
4599153--4599221	30	2.3	30	82	9	79	49	2	2	44	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4599143--4599198	21	2.7	21	81	8	62	46	3	3	46	1.37
4600604--4600652	2	24.5	2	95	0	89	46	0	0	53	1.00
4600830--4600862	17	1.9	18	88	11	52	51	0	0	48	1.00
4604221--4604261	17	2.5	16	82	17	57	48	2	0	48	1.14
4604692--4604928	105	2.3	105	90	2	361	48	2	3	45	1.32
4609201--4609335	69	2.0	68	83	4	173	45	3	9	41	1.55
4611495--4611699	50	4.1	50	89	0	320	29	21	19	30	1.97
4614700--4614958	50	5.2	50	86	0	358	30	20	18	30	1.96
4621348--4621437	28	3.4	26	77	8	92	44	21	7	26	1.79
4621619--4621645	8	3.4	8	100	0	54	37	0	11	51	1.37
4621588--4621624	2	18.5	2	100	0	74	51	0	0	48	1.00
4622023--4622049	2	13.5	2	100	0	54	51	0	0	48	1.00
4622435--4622479	21	2.1	22	83	4	56	42	0	4	53	1.21
4624083--4624134	24	2.1	25	85	7	70	48	0	1	50	1.12
4625988--4626058	27	2.6	27	88	6	99	46	23	7	22	1.76
4630562--4630632	27	2.6	27	88	6	99	46	23	7	22	1.76
4632859--4633008	50	3.0	50	88	5	205	33	20	14	32	1.92
4637461--4637608	50	3.0	50	88	0	206	29	19	18	32	1.96
4638552--4638592	21	2.0	20	85	4	55	53	2	0	43	1.13
4639318--4639382	16	3.9	17	79	16	75	33	3	1	61	1.21
4639309--4639378	16	4.4	16	78	18	74	34	2	1	61	1.20
4640558--4640603	17	2.8	16	78	18	58	47	0	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4640564--4640620	16	3.5	17	76	13	57	56	0	0	43	0.99
4641057--4641272	106	2.0	106	95	1	389	48	2	3	46	1.31
4641078--4641301	107	2.1	107	84	3	281	51	3	3	42	1.33
4643488--4643530	12	3.4	12	80	6	50	39	0	6	53	1.28
4646426--4646468	2	21.5	2	100	0	86	51	0	0	48	1.00
4647963--4647998	2	18.0	2	100	0	72	50	0	0	50	1.00
4655234--4655263	2	15.0	2	92	0	51	50	0	3	46	1.18
4656854--4656884	13	2.3	14	94	5	55	45	0	3	51	1.17
4656865--4656923	29	2.0	30	93	3	102	44	0	0	55	0.99
4656854--4656915	14	4.4	14	72	8	54	45	0	1	53	1.10
4657948--4657985	2	19.0	2	100	0	76	0	50	0	50	1.00
4659272--4659308	2	18.5	2	88	0	56	45	0	5	48	1.25
4663384--4663431	25	1.9	25	95	0	87	35	8	14	41	1.76
4667394--4667419	2	13.0	2	100	0	52	50	0	0	50	1.00
4667417--4667443	4	6.8	4	100	0	54	25	0	22	51	1.48
4669059--4669088	2	15.0	2	100	0	60	50	0	0	50	1.00
4678522--4678554	2	16.5	2	100	0	66	0	51	0	48	1.00
4685613--4685777	86	1.9	85	88	3	251	34	16	17	30	1.93
4686921--4686952	2	16.0	2	93	0	55	50	3	0	46	1.17
4693363--4693420	30	1.9	30	100	0	116	36	12	3	48	1.57
4693712--4693751	19	2.1	19	86	9	55	40	0	0	60	0.97
4693695--4693787	25	3.7	26	72	13	70	40	1	0	58	1.05
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4694019--4694064	23	2.1	21	84	8	56	50	4	2	43	1.34
4694916--4694971	22	2.6	22	75	8	53	51	0	0	48	1.00
4697335--4697361	2	13.5	2	100	0	54	51	0	0	48	1.00
4697961--4697995	12	2.9	12	91	0	61	82	0	0	17	0.66
4699874--4699898	2	12.5	2	100	0	50	48	0	0	52	1.00
4703086--4703177	23	3.8	23	74	17	71	45	0	0	54	0.99
4703096--4703194	32	2.9	33	83	10	121	42	0	0	57	0.98
4703096--4703185	33	2.7	32	88	8	119	44	0	0	55	0.99
4703059--4703191	41	3.5	39	74	20	129	42	0	0	57	0.98
4703095--4703201	33	3.2	32	75	18	96	40	0	0	59	0.97

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