oyster.v9_M.fa.s25.2.7.7.80.10.50.500.1.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: scaffold393
Parameters: 2 7 7 80 10 50 500
Length:  1263635

Tables:   1   2   3   4   

This is table  1  of  4  ( 399 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)
5534--5666	70	1.9	69	87	4	196	30	15	12	41	1.84
5823--5882	2	30.0	2	100	0	120	50	0	50	0	1.00
6008--6078	2	36.0	2	94	2	117	1	46	0	52	1.09
23370--23485	23	5.0	23	97	0	223	17	26	20	35	1.95
38150--38227	33	2.5	31	76	17	88	20	12	34	32	1.90
38901--38947	23	2.0	23	100	0	94	29	12	12	44	1.80
40209--40251	2	21.5	2	100	0	86	0	0	51	48	1.00
43207--43610	200	2.0	200	100	0	808	37	16	19	25	1.93
43683--43761	34	2.3	35	91	8	135	44	16	10	29	1.80
47060--47140	2	40.5	2	100	0	162	0	49	0	50	1.00
47613--47769	21	7.4	21	79	8	167	38	17	7	36	1.78
47613--47745	63	2.1	63	88	2	196	36	18	6	39	1.75
48704--48973	21	12.9	21	78	3	240	40	7	15	37	1.75
51699--51753	2	27.5	2	96	0	101	50	1	47	0	1.11
51835--51894	2	30.0	2	100	0	120	50	0	50	0	1.00
52223--52250	3	9.3	3	100	0	56	35	32	0	32	1.58
53347--53377	16	1.9	16	93	0	53	16	22	12	48	1.80
54094--54184	27	3.4	26	84	3	101	35	12	25	27	1.91
56866--56916	21	2.4	21	96	0	93	19	17	13	49	1.80
74809--75406	145	4.2	144	77	7	552	30	19	20	29	1.97
76391--76460	2	35.5	2	97	2	133	0	48	0	51	1.00
76557--76604	2	24.0	2	100	0	96	0	50	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
79998--80388	196	2.0	195	98	0	755	37	17	13	30	1.89
84391--84542	34	4.5	34	73	3	108	29	9	25	34	1.88
84372--84559	102	1.8	102	89	2	297	28	8	25	37	1.85
84556--84697	68	2.1	68	94	0	248	28	7	26	37	1.83
84556--84681	34	3.7	34	97	0	243	30	7	26	36	1.83
87814--88286	251	1.9	253	95	0	869	41	15	9	34	1.79
92394--92433	17	2.3	18	86	4	55	47	2	12	37	1.55
94026--94202	91	1.9	91	97	0	336	38	11	16	33	1.84
100303--100408	34	3.1	34	90	2	151	20	3	33	42	1.70
100402--100479	34	2.3	34	82	4	86	28	3	26	41	1.73
108397--108450	2	27.0	2	100	0	108	0	50	0	50	1.00
108577--108603	12	2.2	12	100	0	54	0	40	0	59	0.98
108735--108778	2	22.0	2	100	0	88	0	50	0	50	1.00
108917--108991	2	37.0	2	97	2	141	0	49	1	49	1.09
109093--109117	12	2.1	12	100	0	50	0	40	0	60	0.97
109376--109439	2	32.0	2	88	0	92	0	48	3	48	1.17
109896--110125	38	6.1	38	96	0	397	43	16	11	29	1.83
109997--110095	19	5.2	19	62	33	52	42	18	10	29	1.82
110318--110360	19	2.3	19	87	0	59	44	9	25	20	1.81
114879--114912	2	17.0	2	100	0	68	0	50	0	50	1.00
114983--115050	2	34.5	2	94	2	120	0	50	0	50	1.00
134656--135761	33	33.1	33	86	3	1444	18	16	22	42	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
135480--135538	19	3.1	19	92	0	100	16	13	23	45	1.83
135447--135708	71	3.8	71	85	5	399	17	15	23	43	1.88
135414--135708	104	2.8	104	84	5	339	18	15	23	43	1.88
135409--135761	137	2.6	137	97	0	652	17	16	23	42	1.88
135617--135675	19	3.1	19	92	0	100	16	13	23	45	1.83
135551--135741	104	1.8	104	97	0	364	17	15	24	42	1.87
136316--136380	2	32.5	2	96	0	121	0	49	0	50	1.00
136540--136612	19	3.8	19	83	0	83	36	17	19	26	1.94
137039--137125	2	43.5	2	88	0	129	0	43	4	51	1.22
138998--139049	2	26.0	2	100	0	104	0	50	0	50	1.00
141122--141149	11	2.5	11	100	0	56	85	14	0	0	0.59
142581--142644	2	32.0	2	96	0	119	0	48	0	51	1.00
143684--143767	2	42.0	2	97	0	159	0	48	0	51	1.00
144737--144780	4	11.2	4	90	4	72	2	22	0	75	0.92
144778--144835	2	29.0	2	82	0	71	5	46	0	48	1.24
146270--146311	2	21.0	2	100	0	84	0	50	0	50	1.00
146386--146621	17	13.8	17	95	1	400	18	19	17	44	1.87
146826--146891	17	3.9	17	100	0	132	18	16	18	46	1.84
146553--147095	271	2.0	271	97	0	1025	24	17	20	37	1.94
147754--147815	2	31.0	2	90	0	97	0	45	0	54	0.99
147815--148221	45	9.0	45	93	0	661	31	16	17	34	1.92
148525--148574	2	25.0	2	100	0	100	0	50	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
153396--153450	27	2.0	27	89	0	83	30	18	18	32	1.95
153613--153710	35	2.8	35	90	0	160	36	5	17	40	1.72
153603--153757	35	4.5	35	80	5	120	30	5	19	43	1.74
153603--153781	70	2.6	70	77	7	168	31	6	19	42	1.77
153753--153887	35	3.8	35	71	7	103	35	7	14	42	1.73
158813--158837	12	2.1	12	100	0	50	32	8	16	44	1.76
161099--161202	53	2.0	53	94	0	181	30	18	22	28	1.97
162011--162171	65	2.5	64	80	4	189	32	13	13	40	1.83
162903--163117	34	6.3	34	81	2	225	26	8	28	35	1.86
163056--163127	34	2.1	34	81	0	81	29	9	26	34	1.88
162907--163142	102	2.3	102	80	2	276	26	8	28	36	1.87
163263--163365	34	3.1	34	73	8	102	28	3	29	38	1.75
169165--169208	22	2.0	22	86	0	61	18	20	13	47	1.82
174827--174877	15	3.4	15	76	10	50	47	13	1	37	1.55
176611--176652	19	2.2	19	86	0	57	40	33	4	21	1.74
176619--176658	19	2.1	19	90	0	62	37	37	2	22	1.68
176548--176925	177	2.1	176	83	4	467	33	25	16	24	1.96
176991--177024	12	2.8	12	95	0	59	14	55	26	2	1.53
182211--182274	33	1.9	34	87	6	96	45	4	10	39	1.60
182799--182865	32	2.3	27	73	26	73	22	28	16	31	1.95
193358--193409	21	2.5	22	84	6	72	38	13	9	38	1.77
198903--198951	2	24.5	2	100	0	98	0	48	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
203186--203244	27	2.2	27	96	0	109	45	10	1	42	1.48
207084--207114	16	1.9	16	93	0	53	25	19	12	41	1.87
206941--207115	93	1.9	93	87	7	257	32	20	17	29	1.96
212345--212371	2	13.5	2	100	0	54	51	0	48	0	1.00
212370--212418	4	11.5	4	79	12	53	28	20	24	26	1.99
212370--212415	13	3.5	13	91	5	67	28	19	23	28	1.98
213696--213720	13	1.9	13	100	0	50	0	8	0	92	0.40
218528--218903	188	2.0	187	98	0	725	31	12	17	38	1.86
219074--220072	438	2.3	438	93	0	1716	36	16	17	30	1.91
222129--222174	2	23.0	2	100	0	92	50	0	50	0	1.00
225206--225235	3	10.0	3	92	0	51	3	30	0	66	1.07
225255--226231	439	2.2	440	92	0	1645	34	17	14	33	1.90
227658--227757	18	5.6	18	86	2	121	41	22	11	26	1.86
227658--227752	36	2.6	36	91	3	147	41	23	10	25	1.86
228867--228915	16	3.3	16	72	21	61	55	12	2	30	1.48
237945--237969	13	1.9	13	100	0	50	32	16	8	44	1.76
239868--240080	104	2.0	104	99	0	417	36	15	13	35	1.86
242756--242814	30	2.0	30	89	0	91	32	28	22	16	1.96
243767--243819	17	3.1	17	77	2	52	20	18	11	49	1.78
255558--255839	150	1.9	151	87	3	417	35	14	9	40	1.78
257002--257335	179	1.9	178	93	1	580	25	21	27	26	1.99
262421--263193	179	4.3	178	90	2	1138	26	24	22	26	2.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
264335--264363	15	1.9	15	100	0	58	41	0	6	51	1.28
265682--265713	4	8.0	4	100	0	64	25	0	0	75	0.81
268441--268495	22	2.5	22	81	0	65	27	12	29	30	1.93
270893--271974	45	24.1	45	89	2	1522	18	21	22	37	1.94
286867--286922	2	28.0	2	100	0	112	0	50	0	50	1.00
287022--287058	18	2.0	19	89	5	58	35	0	10	54	1.36
287935--288005	33	2.2	33	89	0	106	33	15	19	30	1.93
294433--294457	1	25.0	1	100	0	50	0	100	0	0	0.00
296905--296987	22	3.8	22	93	0	130	20	25	32	21	1.98
299405--300033	315	2.0	314	100	0	1249	33	15	21	29	1.94

Tables:   1   2   3   4