oyster.v9_M.fa.s49.2.7.7.80.10.50.500.1.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: scaffold1188
Parameters: 2 7 7 80 10 50 500
Length:  1075576

Tables:   1   2   3   

This is table  1  of  3  ( 317 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)
5407--5450	22	2.0	22	86	0	61	52	25	9	13	1.70
7475--7560	28	2.9	28	77	12	91	39	24	32	3	1.72
7472--7547	32	2.4	32	81	0	89	39	23	32	3	1.73
13163--13200	1	38.0	1	89	0	58	0	5	0	94	0.30
13159--13200	16	2.8	15	89	10	68	0	7	0	92	0.37
16909--17062	39	3.9	39	84	0	182	25	16	21	37	1.93
16909--17056	78	1.9	78	87	0	215	25	16	22	35	1.95
17086--17119	17	2.0	17	88	11	52	41	23	0	35	1.55
25519--25544	13	2.0	13	100	0	52	30	23	15	30	1.95
27518--27562	17	2.9	15	83	6	54	44	11	15	28	1.81
27520--27562	15	2.6	17	82	7	54	44	11	16	27	1.82
31926--31972	2	23.5	2	100	0	94	0	48	0	51	1.00
35612--35661	2	25.0	2	100	0	100	50	0	50	0	1.00
58231--58351	30	4.0	30	97	0	224	23	25	26	24	2.00
63159--63228	32	2.2	32	87	2	97	42	8	8	40	1.66
64311--64335	13	1.9	13	100	0	50	44	24	0	32	1.54
67063--67095	17	1.9	17	100	0	66	21	48	6	24	1.72
68486--68522	18	2.0	18	89	5	56	32	32	29	5	1.80
86911--86948	5	7.6	5	87	0	58	47	18	0	34	1.49
105390--105422	17	1.9	17	100	0	66	24	27	18	30	1.98
105389--105425	17	2.2	17	90	0	65	24	24	16	35	1.95
105672--105728	23	2.5	23	82	5	71	21	12	19	47	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
105802--105854	23	2.3	24	81	15	67	41	20	9	28	1.83
105856--105906	22	2.3	23	86	3	68	37	19	13	29	1.90
106070--106127	23	2.5	23	80	0	62	39	17	18	24	1.92
107292--107387	23	4.2	23	78	1	86	29	16	20	33	1.95
107283--107395	45	2.5	45	77	11	115	27	16	20	35	1.94
107439--107482	23	1.9	23	90	0	70	34	15	11	38	1.84
110305--110337	17	1.9	17	100	0	66	45	6	12	36	1.66
111361--111393	17	1.9	17	100	0	66	24	21	24	30	1.99
112828--114204	22	62.5	22	81	7	985	25	27	9	36	1.88
112866--114204	66	20.3	66	82	5	1384	25	27	9	36	1.88
113207--113308	53	1.9	53	85	0	141	22	27	11	38	1.89
140291--140335	19	2.4	20	78	17	51	48	11	15	24	1.77
156101--156223	64	1.9	64	96	0	228	33	18	17	30	1.95
159155--159273	51	2.3	51	86	0	166	12	31	26	29	1.93
162435--162553	38	3.2	38	62	11	100	31	18	18	31	1.95
162413--162558	75	1.9	75	100	0	292	31	17	20	30	1.95
164496--164524	14	2.0	15	93	6	51	68	0	10	20	1.18
167783--167812	11	2.8	11	95	5	53	93	6	0	0	0.35
177033--177142	40	2.8	40	97	0	202	40	22	15	21	1.91
177069--177133	20	3.2	20	63	16	53	40	21	15	23	1.91
177850--177904	15	3.7	15	97	0	101	16	16	30	36	1.91
177850--177912	30	2.1	30	88	5	92	20	15	30	33	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
177893--177954	21	3.0	21	95	0	106	25	14	30	29	1.95
178087--178115	12	2.3	13	94	5	51	34	17	34	13	1.89
207270--207377	33	3.3	33	87	3	155	16	25	23	34	1.95
215427--215458	16	2.0	16	93	0	55	31	9	25	34	1.87
216941--217021	41	2.0	40	87	2	117	30	6	12	50	1.64
218726--218774	21	2.3	22	82	7	64	42	14	18	24	1.87
229295--229339	2	23.0	2	88	4	56	0	53	0	46	1.00
254402--254426	6	4.2	6	100	0	50	84	16	0	0	0.63
256335--256414	21	3.8	21	86	4	90	26	8	23	41	1.83
256335--256414	42	1.9	42	84	5	108	26	8	23	41	1.83
256438--256471	15	2.3	15	89	0	50	23	8	26	41	1.83
256669--256744	21	3.6	21	78	3	82	27	11	23	36	1.90
263550--263590	20	2.0	20	90	9	66	26	14	4	53	1.61
269150--269209	4	15.8	4	83	10	65	0	0	21	78	0.75
269143--269228	39	2.3	38	86	6	122	0	1	20	77	0.83
269148--269227	8	10.4	8	71	12	60	0	1	20	78	0.81
279964--280011	4	12.0	4	90	0	78	75	2	0	22	0.91
288651--288728	21	3.7	21	87	3	113	38	30	12	17	1.88
290624--290882	130	2.0	129	99	0	500	29	27	12	30	1.93
291936--291966	15	2.0	16	93	6	55	19	12	35	32	1.90
297271--297443	62	2.8	62	100	0	346	35	17	18	27	1.94
304199--304316	43	2.7	43	83	5	123	37	11	16	34	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
304159--304316	86	1.8	86	80	2	192	36	12	15	35	1.85
308354--308394	19	2.1	20	86	4	57	4	17	19	58	1.56
309161--309217	22	2.6	22	91	0	87	24	14	17	43	1.86
309251--309295	19	2.4	20	85	7	58	4	17	20	57	1.56
309260--309297	19	2.0	19	90	10	60	0	18	21	60	1.36
310313--310383	22	3.3	22	72	18	67	46	4	9	39	1.57
310317--310402	43	2.0	43	93	0	145	45	4	10	39	1.59
313457--313485	12	2.4	12	100	0	58	0	34	17	48	1.47
313734--313766	15	2.2	15	94	0	57	51	9	15	24	1.72
314198--315453	331	3.7	331	85	5	1594	26	24	16	32	1.96
314191--315453	165	7.5	166	84	5	1596	26	24	16	32	1.96
317813--317862	8	6.4	8	86	4	75	38	26	36	0	1.57
320849--320946	47	2.1	47	94	1	171	40	13	7	38	1.72
321984--322049	8	7.8	8	76	18	62	1	10	4	83	0.86
321985--322050	26	2.6	25	81	13	80	1	10	6	81	0.92
321981--322049	18	3.8	18	81	5	61	1	11	4	82	0.87
326240--326269	2	15.0	2	92	0	51	0	0	53	46	1.00
332400--332457	4	14.5	4	96	0	107	51	0	22	25	1.48
340345--340985	326	2.0	327	90	2	1011	27	25	19	27	1.99
340877--341101	116	1.9	116	96	0	414	27	26	22	24	2.00
341668--341692	13	1.9	13	100	0	50	8	16	36	40	1.77
345464--345497	16	2.1	16	94	0	59	32	29	8	29	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
347209--347260	2	26.0	2	100	0	104	0	50	0	50	1.00
354974--354999	13	2.0	13	100	0	52	53	7	23	15	1.67
355289--355322	12	2.8	12	90	4	50	0	17	32	50	1.47
355289--355322	15	2.5	13	90	9	50	0	17	32	50	1.47
355479--356445	159	6.1	160	79	8	854	34	15	20	29	1.93
355946--356224	153	1.8	153	85	3	400	36	15	18	29	1.92
355547--356317	312	2.4	314	87	6	1069	34	15	21	28	1.94
356099--356445	156	2.2	157	81	7	382	37	14	19	28	1.91
360499--360565	31	2.1	33	88	5	102	32	28	16	22	1.95
369054--369092	20	1.9	20	90	10	62	25	20	12	41	1.88
369130--369685	280	2.0	280	97	0	1058	32	14	19	33	1.92
389664--389744	28	2.8	29	83	3	110	27	24	13	34	1.93
389624--389757	28	4.7	28	78	5	99	24	24	15	35	1.94
392317--392354	3	12.7	3	88	0	58	36	2	28	31	1.71
392714--392758	2	22.5	2	95	0	81	0	46	0	53	1.00
392820--392867	2	24.0	2	100	0	96	0	50	0	50	1.00
393108--393138	2	15.5	2	100	0	62	0	51	0	48	1.00
393868--393922	21	2.5	22	72	21	53	38	3	5	52	1.42
400211--400240	2	15.0	2	92	0	51	50	46	0	3	1.18
405368--405435	21	3.2	21	71	8	57	32	17	17	32	1.94
407301--407348	20	2.4	20	82	0	60	33	4	16	45	1.67
407650--407708	20	3.0	20	87	5	84	54	15	0	30	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
426333--426918	290	2.0	291	92	1	989	41	15	10	32	1.81
438920--438952	16	2.1	16	100	0	66	48	27	6	18	1.71
455060--455089	10	3.0	10	100	0	60	40	0	10	50	1.36
471355--471380	1	26.0	1	100	0	52	0	0	100	0	0.00
473408--473461	27	2.0	27	96	0	99	27	11	27	33	1.91
479592--480320	180	4.0	180	93	1	1217	30	14	18	36	1.91
479592--480320	364	2.0	361	92	1	1219	30	14	18	36	1.91
480655--480747	2	46.5	2	100	0	186	49	0	50	0	1.00
481444--481521	20	3.9	20	96	0	138	25	15	29	29	1.96
501204--501796	172	3.4	172	93	1	999	35	15	19	30	1.92

Tables:   1   2   3