oyster.v9_M.fa.s34.2.7.7.80.10.50.500.1.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.04

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: scaffold678
Parameters: 2 7 7 80 10 50 500
Length:  1173314

Tables:   1   2   3   4   

This is table  1  of  4  ( 461 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)
3080--3108	2	15.0	2	92	7	51	0	51	0	48	1.00
11067--11112	11	4.0	11	88	11	58	8	17	26	47	1.76
11067--11112	24	2.0	22	91	8	74	8	17	26	47	1.76
11120--11150	11	2.8	11	90	0	53	45	29	16	9	1.79
11358--11391	11	3.2	10	84	15	50	50	29	11	8	1.69
17311--17352	18	2.3	18	91	0	66	35	9	0	54	1.33
17311--17370	6	10.0	6	79	0	57	35	10	0	55	1.34
23352--23389	2	20.0	2	89	10	62	47	0	52	0	1.00
27931--27993	2	31.5	2	100	0	126	0	50	0	49	1.00
34654--34686	2	16.5	2	100	0	66	51	0	48	0	1.00
38987--39012	12	2.2	12	100	0	52	26	15	0	57	1.38
41315--41345	11	2.8	11	95	0	53	32	25	6	35	1.82
43560--43595	2	17.5	2	94	5	63	50	0	2	47	1.15
45365--45420	21	2.7	21	97	0	103	41	5	30	23	1.76
50124--50177	21	2.6	21	87	0	81	40	7	29	22	1.81
53505--53539	2	17.5	2	100	0	70	0	51	0	48	1.00
57099--57170	11	6.7	11	71	4	58	25	26	9	38	1.86
57099--57170	21	3.4	21	73	3	72	25	26	9	38	1.86
59065--59093	15	1.9	15	100	0	58	27	31	27	13	1.94
61339--61390	12	4.5	11	83	9	68	86	11	1	0	0.65
61341--61379	6	6.8	6	94	5	64	84	15	0	0	0.62
61342--61389	16	2.9	16	80	20	55	85	12	2	0	0.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
65312--65338	13	2.1	13	100	0	54	29	18	22	29	1.97
67262--67577	156	2.0	157	98	0	607	40	13	14	32	1.84
72359--72419	2	30.5	2	100	0	122	0	50	0	49	1.00
88817--88935	60	2.0	59	93	3	195	44	14	15	24	1.84
97648--97936	28	10.4	28	79	4	273	20	27	14	38	1.91
97648--97936	83	3.5	83	77	3	231	20	27	14	38	1.91
97648--97957	55	5.6	55	77	4	300	20	27	14	38	1.91
98192--98236	2	22.5	2	100	0	90	0	48	0	51	1.00
99160--99192	17	1.9	17	88	11	50	18	15	0	66	1.25
104329--104368	21	1.9	21	85	10	55	72	2	22	2	1.09
104735--105731	438	2.3	437	90	1	1516	31	18	15	34	1.92
106344--106579	58	4.0	62	75	11	208	48	15	20	15	1.81
114020--114044	1	25.0	1	100	0	50	0	100	0	0	0.00
116673--116739	2	33.5	2	100	0	134	0	49	0	50	1.00
116960--117161	110	1.8	110	93	0	350	37	15	16	30	1.90
116965--117188	110	2.0	110	85	1	295	35	17	19	28	1.94
121380--121436	12	4.8	12	93	2	89	0	35	26	38	1.57
121379--121436	4	14.8	4	83	3	55	0	34	25	39	1.56
121606--121957	170	2.1	166	93	3	598	31	17	24	26	1.97
123522--123559	15	2.6	15	87	4	51	5	7	0	86	0.69
123708--123741	4	8.5	4	93	0	59	47	26	26	0	1.53
134597--135008	206	2.0	205	99	0	815	29	10	19	39	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
148396--148423	12	2.3	12	100	0	56	42	25	7	25	1.80
160134--160175	2	21.0	2	95	0	75	0	2	50	47	1.14
177647--177982	42	8.0	42	87	4	378	34	36	7	22	1.81
177647--177982	126	2.7	125	85	4	469	34	36	7	22	1.81
179856--179905	24	2.1	24	84	0	64	72	0	16	12	1.13
181389--181418	15	2.0	15	93	0	51	16	33	36	13	1.88
193990--194048	2	30.0	2	96	3	111	0	49	0	50	1.00
194348--194384	14	2.7	15	88	12	53	81	18	0	0	0.70
194342--194385	21	2.1	20	84	12	54	84	15	0	0	0.63
197598--197627	11	2.8	11	95	5	53	93	0	6	0	0.35
201146--201174	15	1.9	15	100	0	58	13	44	20	20	1.85
205860--205903	4	11.0	4	95	0	70	0	29	25	45	1.54
205861--205910	24	2.1	24	100	0	100	0	32	26	42	1.56
205934--207060	166	6.8	166	88	2	1602	29	17	14	38	1.90
205934--207060	333	3.4	333	91	0	1767	29	17	14	38	1.90
218075--218106	2	16.0	2	100	0	64	50	0	50	0	1.00
219690--219743	2	27.0	2	100	0	108	50	0	50	0	1.00
220893--220957	32	2.0	32	87	0	94	27	27	6	38	1.80
221073--221125	2	26.5	2	100	0	106	49	0	50	0	1.00
229761--229806	2	23.0	2	100	0	92	0	50	0	50	1.00
229806--229832	2	13.5	2	100	0	54	48	0	0	51	1.00
241854--242800	438	2.2	438	92	0	1592	29	16	15	37	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
255036--255062	13	2.1	13	100	0	54	70	7	0	22	1.12
256761--256809	24	2.0	24	84	7	64	69	14	0	16	1.19
260539--260816	68	4.1	68	94	0	466	20	19	24	34	1.96
261878--261912	17	2.1	17	94	0	61	34	17	2	45	1.63
272854--272934	21	3.9	22	76	7	71	34	22	20	22	1.97
273042--273112	6	12.0	6	74	14	58	1	0	18	80	0.79
273038--273107	8	7.8	9	76	17	58	1	0	18	80	0.80
273040--273112	22	3.4	22	81	11	71	1	0	17	80	0.78
273040--273112	9	7.9	9	75	13	60	1	0	17	80	0.78
283827--283864	8	4.8	8	93	0	67	39	26	34	0	1.57
283827--283872	16	2.9	16	93	3	76	41	26	32	0	1.56
283830--283872	4	11.0	4	82	5	52	41	25	32	0	1.56
286645--286688	22	2.0	22	100	0	88	27	9	27	36	1.87
287226--287272	18	2.6	18	89	0	67	25	21	12	40	1.89
287811--287857	18	2.6	18	86	6	60	42	12	19	25	1.86
290539--290586	2	24.0	2	95	0	87	2	50	0	47	1.12
299725--300087	182	2.0	181	100	0	717	31	14	22	31	1.93
311706--311733	14	2.0	14	100	0	56	42	14	14	28	1.84
325092--325628	180	3.0	180	97	0	1011	37	15	16	30	1.91
338555--338584	15	2.1	14	93	6	51	0	0	10	90	0.47
338552--338584	11	2.8	12	95	4	59	0	0	12	87	0.53
345958--346033	21	3.7	21	76	15	77	36	11	11	39	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
346001--346053	20	2.6	21	82	11	58	43	9	11	35	1.73
346091--346140	20	2.5	20	77	12	57	40	12	8	40	1.72
346892--346985	20	4.7	21	71	18	74	42	10	14	31	1.80
347125--347215	20	4.4	21	76	18	77	37	13	10	38	1.80
347506--347600	39	2.4	40	92	1	156	35	13	17	32	1.89
347547--347618	21	3.5	20	72	14	58	36	13	16	33	1.89
347508--347626	39	3.0	41	86	9	142	36	15	17	31	1.91
355263--355310	24	2.0	24	92	8	80	43	6	8	41	1.60
364451--364492	22	1.9	22	85	9	59	30	19	16	33	1.94
369153--369186	12	2.8	12	86	0	50	23	11	2	61	1.43
369188--369217	12	2.5	12	100	0	60	0	23	0	76	0.78
372307--372337	15	2.1	15	93	0	53	3	25	0	70	1.02
373145--373276	47	2.8	47	84	2	147	28	33	21	16	1.95
375975--376161	90	2.1	85	93	4	311	45	13	11	28	1.79
376145--376202	20	2.9	20	81	0	71	43	20	8	27	1.81
386718--386747	3	10.0	3	100	0	60	0	33	0	66	0.92
388908--389223	174	1.8	174	80	7	390	28	25	13	32	1.93
397456--397922	27	17.3	27	91	0	702	29	15	30	24	1.96
397921--398929	27	37.4	27	90	0	1462	28	15	31	24	1.96
397854--397989	67	2.0	67	89	0	209	26	17	30	25	1.97
402404--403307	33	25.8	33	81	10	962	42	10	23	24	1.84
402439--403265	110	7.8	108	82	10	815	41	10	23	24	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
402638--403307	176	3.9	165	86	7	890	41	10	23	24	1.85
402539--403307	209	3.7	209	87	4	1018	42	10	23	24	1.85
403213--403476	35	7.3	35	82	10	271	45	8	20	25	1.80
403247--403471	76	2.9	77	85	3	285	46	8	20	24	1.78
403700--403753	25	2.2	25	86	3	74	27	27	16	27	1.97
408808--408852	19	2.4	18	86	13	65	37	13	22	26	1.91
408815--408855	19	2.1	20	95	4	75	41	14	19	24	1.89
411084--411215	30	4.4	30	95	1	221	31	17	6	43	1.75
411712--412136	39	11.4	39	73	13	338	26	13	22	37	1.92
411717--411917	107	1.9	108	88	2	305	24	14	22	37	1.92

Tables:   1   2   3   4