oyster.v9_M.fa.s33.2.7.7.80.10.50.500.1.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: scaffold100
Parameters: 2 7 7 80 10 50 500
Length:  1174989

Tables:   1   2   3   4   

This is table  1  of  4  ( 392 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)
4539--4937	199	2.0	198	99	0	789	30	15	14	39	1.87
5003--5036	2	17.0	2	93	0	59	52	0	0	47	1.00
11925--12931	28	38.0	28	79	11	1086	42	17	14	25	1.87
11921--12916	52	18.8	52	86	7	1046	42	17	14	25	1.87
11921--12931	211	4.8	211	86	7	1061	42	17	14	25	1.87
17395--17432	2	19.0	2	94	0	67	50	2	47	0	1.15
17766--17796	2	15.5	2	100	0	62	51	0	48	0	1.00
19048--19087	2	20.0	2	100	0	80	0	0	50	50	1.00
19087--19128	2	21.0	2	100	0	84	50	0	50	0	1.00
22137--22179	12	3.6	12	87	0	59	0	30	25	44	1.55
22137--22172	4	9.0	4	93	0	63	0	27	25	47	1.52
26390--26434	2	22.5	2	100	0	90	0	0	51	48	1.00
26828--27103	140	2.0	141	96	0	509	38	15	14	31	1.88
27071--27135	33	2.0	32	90	3	103	43	24	9	23	1.83
34742--34870	30	4.3	30	90	3	179	25	24	23	27	2.00
34764--34869	15	7.1	15	62	12	56	25	23	24	26	2.00
34740--34873	60	2.2	60	90	0	205	25	23	23	26	2.00
34755--34873	30	4.0	30	94	0	202	25	24	25	25	2.00
35558--35601	22	2.0	22	100	0	88	36	13	13	36	1.85
38711--38859	30	5.0	30	95	0	253	25	24	25	24	2.00
39544--39587	22	2.0	22	100	0	88	36	13	13	36	1.85
43045--43146	4	25.5	4	95	0	186	24	27	0	48	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
45820--45925	55	1.9	55	100	0	212	25	22	10	41	1.85
45877--46228	167	2.1	168	78	7	387	32	19	17	31	1.94
49155--49248	46	2.0	46	91	0	152	23	17	19	40	1.91
49792--49822	16	1.9	16	93	0	53	45	29	6	19	1.75
51702--51750	2	24.5	2	100	0	98	51	0	48	0	1.00
55943--55973	15	2.0	16	93	6	55	38	0	9	51	1.35
57048--57072	1	25.0	1	100	0	50	100	0	0	0	0.00
60373--60447	33	2.3	33	90	2	125	26	16	24	33	1.95
63494--63527	17	2.1	16	94	5	59	47	5	5	41	1.52
63814--63925	56	2.0	55	98	1	215	30	7	17	43	1.76
73811--73874	2	32.0	2	100	0	128	0	0	50	50	1.00
83033--83302	35	7.7	35	94	1	445	32	14	12	40	1.83
83361--83511	40	3.7	40	94	3	248	39	17	12	30	1.87
90396--90430	2	17.5	2	100	0	70	0	51	0	48	1.00
92372--92396	2	12.5	2	100	0	50	52	0	48	0	1.00
96516--96638	30	4.1	30	93	0	210	42	20	21	15	1.89
97372--97423	21	2.5	21	87	0	77	28	15	26	28	1.96
98679--98720	2	21.0	2	90	0	57	0	47	0	52	1.00
104320--104850	46	11.6	46	81	4	488	27	26	15	30	1.96
104335--104834	92	5.5	92	82	2	558	27	25	15	30	1.96
104316--104834	138	3.8	138	82	2	596	27	25	15	30	1.96
108526--108565	21	1.9	21	89	0	62	32	17	12	37	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
115915--115945	15	2.1	15	100	0	62	58	16	0	25	1.38
117309--117342	9	3.7	9	84	7	50	2	0	73	23	0.97
117316--117350	10	3.6	10	84	7	54	5	0	65	28	1.15
117309--117350	19	2.2	19	100	0	84	4	0	69	26	1.08
123548--124085	11	53.6	11	77	17	541	48	16	14	21	1.81
123561--124085	30	17.5	30	79	14	443	48	16	14	21	1.81
123590--124106	19	27.0	19	79	13	491	47	16	14	21	1.81
124624--126170	16	95.1	16	75	7	1218	29	10	20	39	1.85
125697--125821	36	3.6	36	74	16	136	23	9	27	40	1.85
127499--127566	2	34.0	2	100	0	136	0	50	0	50	1.00
127773--127823	2	25.5	2	95	0	93	52	0	47	0	1.00
128590--128640	25	2.0	25	100	0	102	25	15	27	31	1.96
130060--130098	21	1.9	20	89	5	60	0	0	15	84	0.62
130062--130097	16	2.2	17	95	5	65	0	0	13	86	0.58
130248--130333	40	2.1	40	100	0	172	27	15	22	34	1.94
130305--130454	30	5.0	30	95	0	264	32	15	19	33	1.93
135155--135213	2	29.5	2	96	0	109	0	47	0	52	1.00
137877--137944	34	2.0	34	97	0	127	35	13	14	36	1.85
137936--138047	35	3.2	34	83	14	140	25	10	17	46	1.80
137948--138045	34	2.9	34	86	4	126	26	9	18	45	1.79
145803--145885	2	42.0	2	97	2	159	0	49	0	50	1.00
148811--148854	1	44.0	1	100	0	88	0	0	0	100	0.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
149303--149345	17	2.4	19	80	7	54	4	9	16	69	1.31
150132--150203	2	36.0	2	97	0	126	52	0	47	0	1.00
150423--150499	24	3.2	24	94	0	136	23	18	37	20	1.94
154527--154555	12	2.4	12	100	0	58	48	17	6	27	1.72
155471--157406	45	43.0	45	92	1	3180	27	19	17	35	1.94
162294--162331	19	2.1	18	90	5	58	0	0	15	84	0.63
164161--164214	2	27.0	2	100	0	108	50	0	50	0	1.00
165725--165770	20	2.3	20	88	7	67	30	10	19	39	1.86
165737--165779	20	2.3	19	88	8	61	25	11	13	48	1.77
180617--181001	21	18.2	21	81	4	371	32	16	14	37	1.88
180626--181003	64	5.9	64	86	3	442	33	16	14	36	1.88
180617--181002	85	4.6	85	84	3	404	32	16	13	37	1.88
180617--181001	43	9.1	42	79	4	371	32	16	14	37	1.88
186422--186478	11	5.0	11	72	8	51	33	21	19	26	1.97
189316--189357	2	21.0	2	100	0	84	50	0	50	0	1.00
189355--189385	4	7.8	4	92	0	53	51	19	25	3	1.62
189355--189389	16	2.2	16	100	0	70	51	17	25	5	1.67
197024--197129	53	2.0	53	83	3	133	23	21	23	31	1.99
197263--197353	16	5.5	16	82	11	112	25	26	25	23	2.00
197944--197982	2	19.5	2	100	0	78	48	0	51	0	1.00
198513--198583	21	3.4	21	90	0	106	36	19	12	30	1.89
198779--198812	10	3.4	10	83	0	50	41	29	8	20	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
198779--198812	15	2.3	15	94	0	59	41	29	8	20	1.82
198836--198915	21	3.8	21	88	4	117	41	23	8	26	1.83
202647--202706	21	2.8	21	80	16	70	33	28	13	25	1.93
202763--202796	17	2.0	17	88	0	50	38	8	20	32	1.84
203661--203707	2	23.5	2	100	0	94	48	0	51	0	1.00
204767--204792	9	2.9	9	100	0	52	23	23	11	42	1.86
218065--218131	7	9.6	7	80	6	82	34	16	22	26	1.95
219185--219584	200	2.0	200	100	0	800	37	14	17	31	1.90
224855--224921	1	67.0	1	96	0	125	0	0	1	98	0.11
226577--226667	4	22.8	4	87	0	83	40	24	34	1	1.62
226578--226667	12	7.5	12	84	0	108	40	24	34	1	1.63
235265--235590	166	2.0	165	98	0	625	42	14	10	33	1.79
235951--235992	20	2.2	19	87	8	59	64	21	4	9	1.42
240881--240941	32	2.0	31	84	9	81	26	8	9	55	1.60
241173--241362	62	2.9	66	82	6	201	48	21	12	17	1.80
242083--242140	26	2.2	27	90	3	91	22	18	8	50	1.74
254357--254409	2	26.5	2	100	0	106	0	49	0	50	1.00
255736--255770	18	1.9	18	88	0	52	40	8	2	48	1.49
256278--256303	13	2.0	13	100	0	52	15	15	15	53	1.73
264343--264369	14	1.9	14	100	0	54	44	25	0	29	1.54
266486--266532	3	15.7	3	100	0	94	31	34	0	34	1.58
279716--279794	36	2.2	36	95	0	140	16	7	15	60	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
279724--279783	17	3.4	17	68	17	50	16	6	13	63	1.50
280739--280774	2	18.0	2	100	0	72	50	0	50	0	1.00
283537--283562	13	2.0	13	100	0	52	46	15	0	38	1.46
287756--287805	18	2.9	18	71	14	52	6	36	0	58	1.23
289174--289219	24	1.9	24	82	8	58	17	26	15	41	1.88
292519--292553	2	17.5	2	100	0	70	51	0	48	0	1.00
292927--293062	68	2.0	67	89	1	209	36	13	22	26	1.92
293358--294097	38	19.6	38	88	5	1049	24	14	23	37	1.93
293609--293663	28	2.0	27	92	0	83	18	18	29	32	1.94
295163--295203	20	2.0	21	85	4	57	39	9	12	39	1.76

Tables:   1   2   3   4