oyster.v9_M.fa.s19.2.7.7.80.10.50.500.1.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: scaffold3
Parameters: 2 7 7 80 10 50 500
Length:  1336734

Tables:   1   2   3   4   

This is table  1  of  4  ( 390 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)
5572--5605	17	2.0	17	100	0	68	29	11	41	17	1.85
29738--29802	2	32.5	2	87	0	94	52	0	47	0	1.00
30130--30161	16	2.0	16	93	0	55	3	40	25	31	1.71
34360--34427	21	3.3	21	81	4	84	26	16	14	42	1.86
34383--34417	13	2.6	14	86	9	54	22	17	17	42	1.88
34362--34427	7	9.6	7	73	3	53	27	16	15	40	1.88
34362--34427	14	4.8	14	80	10	64	27	16	15	40	1.88
38305--38371	7	9.6	7	83	0	89	35	14	22	26	1.93
40023--40101	32	2.4	32	93	2	140	27	29	17	25	1.98
41103--41420	166	2.0	150	86	10	431	40	12	10	32	1.77
54437--54524	45	1.9	46	88	2	133	38	12	14	34	1.84
56926--56974	8	6.2	8	92	2	73	34	26	38	0	1.57
56926--56968	4	10.8	4	84	0	59	32	25	41	0	1.56
60044--60110	1	67.0	1	75	0	62	1	0	10	88	0.59
60044--60107	12	5.5	11	85	10	76	1	0	10	87	0.61
60044--60110	30	2.3	29	89	7	100	1	0	10	88	0.59
66365--66445	14	5.8	14	76	5	74	22	32	16	29	1.95
66369--66436	21	3.2	21	91	0	109	20	32	16	30	1.94
67797--67835	13	2.9	14	80	7	53	28	15	30	25	1.96
67885--67922	13	2.7	15	88	12	62	13	0	0	86	0.56
67887--67923	17	2.3	16	90	9	58	10	0	0	89	0.49
76661--76689	13	2.1	14	93	6	51	13	0	3	82	0.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
78833--78931	21	4.8	21	92	1	164	28	22	6	43	1.77
78908--79002	42	2.2	42	85	5	120	36	13	11	37	1.81
78973--79073	21	4.6	21	78	11	103	43	5	21	28	1.76
79351--79384	17	2.0	17	94	0	59	26	44	5	23	1.76
79616--79684	21	3.3	21	87	0	102	34	17	7	40	1.77
79666--79754	42	2.1	42	85	8	119	37	12	14	35	1.84
79687--79784	21	4.7	21	79	0	70	34	10	16	38	1.82
79791--79863	21	3.6	21	85	7	114	31	23	4	41	1.73
79861--79913	20	2.6	20	90	3	88	43	5	18	32	1.74
89217--89363	69	2.0	71	88	7	217	33	10	11	44	1.74
108464--108583	44	2.8	43	87	5	170	24	15	12	47	1.80
139365--139390	5	5.2	5	100	0	52	38	23	38	0	1.55
142641--142724	27	3.1	27	67	14	66	20	7	23	48	1.74
142643--142770	51	2.5	51	82	10	156	17	8	24	49	1.75
142582--142778	25	7.7	25	73	10	148	18	8	21	51	1.72
143649--143685	15	2.5	15	95	0	65	35	18	13	32	1.90
150923--150992	35	2.0	34	94	2	122	45	11	12	28	1.77
151077--151102	2	13.0	2	100	0	52	0	50	0	50	1.00
151614--151701	10	8.6	10	73	12	54	23	19	44	12	1.85
151602--151688	20	4.2	20	78	11	86	24	17	43	14	1.86
151771--151820	21	2.5	20	83	3	64	36	12	42	10	1.76
155042--155067	13	2.0	13	100	0	52	46	0	15	38	1.46
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
159474--159831	182	2.0	180	93	2	614	32	19	17	30	1.95
160299--160332	13	2.6	13	90	0	50	29	17	2	50	1.61
166462--166501	12	3.3	12	85	0	62	40	22	35	2	1.68
168049--168080	2	16.5	2	93	6	57	0	50	0	50	1.00
168106--168158	2	26.5	2	96	0	97	0	47	0	52	1.00
168025--168138	57	2.0	58	96	1	212	8	37	3	50	1.51
170095--170174	21	3.8	21	81	0	97	43	16	27	12	1.83
170135--170199	32	2.0	32	90	0	103	46	15	26	12	1.81
170117--170228	53	2.1	53	86	0	161	44	15	25	15	1.85
170051--170227	74	2.4	72	82	7	216	45	14	26	14	1.82
170167--170227	21	2.9	21	87	0	86	45	11	26	16	1.81
171756--171797	20	2.1	20	91	8	68	33	16	19	30	1.94
172734--172776	22	2.0	22	90	0	68	25	25	16	32	1.96
176384--176784	180	2.2	183	83	4	497	39	16	11	31	1.85
176787--176865	39	2.0	39	92	0	131	39	18	5	36	1.73
188565--188590	4	6.5	4	100	0	52	46	26	0	26	1.53
191497--191528	17	1.9	16	93	6	55	56	3	15	25	1.54
191721--191754	2	17.0	2	100	0	68	50	0	50	0	1.00
191986--192022	2	18.5	2	100	0	74	0	51	0	48	1.00
193710--193771	2	32.0	2	93	6	110	0	51	0	48	1.00
195402--195428	1	27.0	1	100	0	54	0	0	0	100	0.00
195561--195598	17	2.1	19	85	9	53	44	15	7	31	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
197002--197079	2	40.0	2	90	10	126	1	48	0	50	1.09
197198--197231	2	17.0	2	93	0	59	2	47	0	50	1.16
200485--200523	21	1.9	21	84	5	53	53	10	2	33	1.48
202974--202998	11	2.3	11	100	0	50	84	8	8	0	0.79
206573--206706	27	4.9	28	90	2	150	43	14	18	23	1.87
206569--206706	56	2.5	55	84	4	154	42	14	18	23	1.88
207516--207545	2	15.0	2	100	0	60	0	50	0	50	1.00
215822--215921	21	4.8	21	77	2	103	17	13	30	40	1.87
218619--218659	16	2.6	16	88	0	64	39	19	36	4	1.73
234493--234593	46	2.1	48	90	7	161	21	11	30	35	1.90
234747--234835	24	3.7	24	82	5	90	17	4	47	30	1.68
234757--234847	24	3.8	24	81	5	94	17	5	45	31	1.71
237364--237388	8	3.1	8	100	0	50	12	0	12	76	1.04
242227--242268	2	21.0	2	95	0	75	47	2	50	0	1.14
245415--245464	22	2.3	22	85	0	64	18	20	14	48	1.82
260713--260781	2	34.5	2	97	0	129	49	0	0	49	1.01
265453--265483	16	1.9	16	93	0	53	45	25	29	0	1.54
265861--265914	21	2.6	21	88	11	92	27	20	9	42	1.82
277302--277333	16	2.0	16	100	0	64	12	18	18	50	1.78
283634--283676	18	2.4	18	84	0	59	23	2	11	62	1.40
284746--284816	32	2.2	32	97	2	133	25	15	19	39	1.91
294251--294288	18	2.1	18	85	9	51	44	7	10	36	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
295073--295106	12	2.9	12	91	4	52	0	29	26	44	1.55
301341--301372	2	16.0	2	100	0	64	50	0	50	0	1.00
308682--308710	10	3.0	10	95	5	51	31	10	10	48	1.71
310559--310601	11	3.9	11	93	0	77	27	32	9	30	1.88
310694--310733	15	2.8	14	85	7	53	87	7	0	5	0.66
322371--322422	2	26.0	2	100	0	104	50	0	50	0	1.00
322609--322637	4	7.2	4	100	0	58	0	24	24	51	1.48
322635--322672	2	19.0	2	100	0	76	0	50	0	50	1.00
323184--323225	7	6.0	7	82	0	57	26	23	14	35	1.93
323184--323225	21	2.0	21	95	0	75	26	23	14	35	1.93
326595--326671	2	38.5	2	94	0	127	48	0	50	1	1.09
339578--340385	161	5.0	159	83	5	856	31	15	19	34	1.93
339649--340385	323	2.3	320	83	4	885	30	15	19	34	1.93
343406--343548	59	2.5	56	87	5	189	21	23	23	32	1.98
345202--345249	2	24.0	2	100	0	96	50	0	50	0	1.00
346951--347066	57	2.0	58	96	1	216	18	21	31	28	1.97
350042--350067	11	2.4	11	100	0	52	30	7	19	42	1.79
355389--355438	2	25.0	2	95	0	91	52	0	48	0	1.00
356558--356595	2	19.0	2	100	0	76	50	0	0	50	1.00
361363--362163	166	4.8	166	93	1	1270	27	22	14	34	1.94
361363--362114	333	2.3	329	93	1	1263	27	23	14	34	1.93
362333--362386	12	4.4	12	80	2	54	46	33	18	1	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
364889--364935	14	3.5	13	83	11	58	6	0	21	72	1.07
364882--364946	17	3.8	17	73	15	53	7	1	20	70	1.19
368083--368128	2	23.0	2	100	0	92	50	0	50	0	1.00
391810--391858	15	3.0	17	82	11	66	36	12	20	30	1.89
392112--392142	16	1.9	16	93	0	53	41	12	22	22	1.88
394730--394754	11	2.3	11	100	0	50	56	0	0	44	0.99
396002--396043	1	42.0	1	95	0	66	0	4	0	95	0.28
396012--396049	20	1.9	20	88	0	58	0	5	5	89	0.59
405362--406028	334	2.0	333	100	0	1325	30	13	25	30	1.93
409718--409918	100	2.0	100	98	1	386	27	24	20	27	1.99

Tables:   1   2   3   4