oyster.v9_M.fa.s2.2.7.7.80.10.50.500.1.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: scaffold1009
Parameters: 2 7 7 80 10 50 500
Length:  1861391

Tables:   1   2   3   4   5   

This is table  1  of  5  ( 553 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)
59--86	1	28.0	1	100	0	56	0	0	100	0	0.00
6657--7018	76	4.8	76	86	2	440	30	16	8	44	1.77
6657--7018	153	2.4	153	84	4	491	30	16	8	44	1.77
9291--9599	96	3.2	96	86	2	399	32	22	15	29	1.95
9712--9912	96	2.1	96	93	0	339	33	20	12	33	1.91
10958--11000	22	2.0	22	85	0	59	44	6	18	30	1.76
12184--12258	36	2.1	36	100	0	150	40	10	13	36	1.79
24789--24823	12	2.7	13	86	13	54	71	5	0	22	1.07
29450--30380	436	2.1	439	87	4	1361	35	15	16	32	1.91
33089--33148	16	3.7	16	77	2	57	51	1	25	21	1.57
33087--33134	4	12.0	4	90	0	60	52	0	29	18	1.46
47757--47808	4	13.5	4	82	8	63	21	1	1	75	1.00
49459--49484	13	2.0	13	100	0	52	38	15	23	23	1.92
54858--54897	20	2.0	20	90	0	62	10	0	57	32	1.32
54864--54902	20	2.0	20	85	5	53	15	0	58	25	1.37
58050--58421	177	2.1	181	90	5	594	29	10	22	37	1.88
62110--62168	2	29.5	2	100	0	118	0	50	0	49	1.00
66585--66746	2	82.0	2	85	7	224	49	0	49	1	1.08
75115--75139	2	12.5	2	100	0	50	48	0	0	52	1.00
93210--93599	18	21.4	18	79	8	396	21	7	28	41	1.81
93774--93848	2	37.5	2	100	0	150	50	0	0	49	1.00
94914--95149	126	1.9	126	99	0	456	44	12	15	27	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
99960--100011	2	26.5	2	96	3	97	0	51	0	48	1.00
101193--101224	12	2.8	11	90	9	55	87	12	0	0	0.54
108832--108873	2	21.0	2	100	0	84	0	50	0	50	1.00
112506--112555	4	12.8	4	91	4	66	32	26	42	0	1.56
116218--116253	4	9.0	4	100	0	72	25	0	25	50	1.50
116308--116348	16	2.6	16	100	0	82	51	0	29	19	1.47
117425--117465	2	20.5	2	94	0	73	53	0	46	0	1.00
127899--127932	15	2.4	15	90	9	54	0	0	11	88	0.52
127893--127933	12	3.2	12	89	6	55	0	0	17	82	0.66
128400--128459	2	30.0	2	100	0	120	0	50	0	50	1.00
131267--131310	23	2.0	21	82	13	52	68	22	4	4	1.27
148675--149434	172	4.4	172	94	0	1288	28	18	15	37	1.91
150949--151023	24	3.1	24	90	0	96	36	21	21	21	1.96
154143--154177	19	1.9	18	88	11	54	48	0	14	37	1.44
159314--159841	165	3.2	164	80	7	507	33	14	23	28	1.94
167429--167578	81	1.9	80	98	0	282	24	15	21	38	1.92
178249--178874	164	3.8	163	90	3	977	28	21	14	34	1.94
179343--179407	31	2.1	30	83	8	78	27	12	16	43	1.84
181923--181960	4	9.5	4	100	0	76	26	23	26	23	2.00
181907--181975	12	5.8	12	85	0	57	37	14	24	23	1.92
181910--181972	8	7.9	8	89	0	63	34	15	25	23	1.95
182225--182251	5	5.4	5	100	0	54	18	40	0	40	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
194990--195434	165	2.7	167	86	2	592	32	19	17	30	1.95
194990--195441	168	2.7	164	85	3	600	32	19	17	30	1.95
197132--197222	4	22.8	4	97	0	164	48	0	27	24	1.51
200878--200924	1	47.0	1	95	0	85	97	0	0	2	0.15
202632--202664	14	2.3	15	94	5	59	0	0	24	75	0.80
204607--204642	11	3.0	12	88	12	56	8	11	25	55	1.62
204607--204644	13	3.1	13	81	14	53	7	10	26	55	1.61
204851--204917	22	3.0	23	72	16	59	10	23	25	40	1.86
204921--204953	13	2.8	12	90	9	50	48	27	15	9	1.74
205687--205772	41	2.1	41	86	0	118	39	15	12	32	1.85
206935--206984	18	2.9	17	85	11	59	56	8	6	30	1.52
208959--208990	15	2.1	16	94	5	57	0	0	43	56	0.99
211515--211592	29	2.8	28	74	3	77	25	11	33	29	1.91
211520--211565	23	2.0	24	86	4	67	26	8	32	32	1.87
220622--220666	23	2.0	22	91	8	72	60	0	6	33	1.23
222867--222897	15	2.1	15	93	0	53	48	0	16	35	1.46
226133--226175	2	21.5	2	100	0	86	48	0	51	0	1.00
226552--226610	2	29.5	2	89	0	82	1	44	0	54	1.10
227465--227522	23	2.6	22	77	2	62	36	12	12	39	1.80
246698--246743	2	23.0	2	100	0	92	0	50	0	50	1.00
255600--255638	2	19.5	2	94	0	69	51	2	46	0	1.14
255600--255650	14	3.6	14	91	0	66	52	5	41	0	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
256496--256564	2	34.5	2	100	0	138	49	0	50	0	1.00
266585--267364	166	4.8	165	86	6	1065	27	23	15	33	1.95
267533--267572	9	4.3	9	93	3	53	52	32	15	0	1.43
267534--267566	15	2.2	15	94	0	57	51	33	15	0	1.43
268418--268528	58	1.9	57	89	3	170	38	14	12	34	1.84
271301--271355	2	27.5	2	100	0	110	50	0	49	0	1.00
274160--274217	6	9.5	6	78	17	66	32	1	13	51	1.51
274164--274208	14	3.3	14	90	6	74	33	2	13	51	1.53
279619--279688	2	35.5	2	97	2	133	0	51	0	48	1.00
280720--280759	20	2.0	20	85	9	55	47	22	0	30	1.52
282274--282386	11	9.7	12	72	14	67	11	14	28	46	1.79
282274--282386	24	4.8	23	77	12	106	11	14	28	46	1.79
282274--282389	35	3.3	35	97	0	223	11	13	27	47	1.77
282298--282387	11	7.8	11	77	18	85	11	14	27	46	1.78
284568--284664	50	2.0	49	91	4	151	16	57	15	9	1.62
285988--286020	17	1.9	17	100	0	66	24	6	48	21	1.72
295999--296042	23	1.9	23	95	0	79	50	9	13	27	1.72
296087--296121	5	6.8	5	96	3	61	0	0	20	80	0.72
296205--296248	23	1.9	23	85	0	61	68	27	4	0	1.09
299098--299144	2	23.5	2	100	0	94	0	48	0	51	1.00
305454--305493	2	20.0	2	100	0	80	0	50	0	50	1.00
317912--317954	2	21.5	2	95	0	77	2	51	0	46	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
319196--319276	2	40.5	2	100	0	162	0	50	0	49	1.00
325230--325272	12	3.7	12	84	6	52	25	18	18	37	1.94
325528--325575	2	24.0	2	100	0	96	0	50	0	50	1.00
331805--331841	11	3.4	11	96	0	65	40	8	8	43	1.64
340275--340319	2	22.5	2	100	0	90	0	51	0	48	1.00
347322--347432	40	2.8	40	94	2	197	32	11	17	38	1.86
357189--357337	41	3.6	42	78	6	142	38	11	11	38	1.77
357204--357337	19	6.5	21	72	13	91	38	10	10	41	1.74
357222--357352	63	2.1	63	83	9	160	39	12	9	38	1.75
357749--357797	2	24.5	2	100	0	98	51	0	48	0	1.00
358336--358372	2	18.5	2	94	0	65	45	0	54	0	1.00
364836--364868	17	1.9	17	100	0	66	24	21	24	30	1.99
370567--370597	16	1.9	16	93	0	53	45	16	16	22	1.85
370813--370845	17	1.9	17	88	11	50	57	0	6	36	1.23
371228--371277	2	25.0	2	100	0	100	0	50	0	50	1.00
371967--372067	21	4.8	21	82	0	112	27	12	16	42	1.85
372139--372228	21	4.3	21	76	0	90	42	15	13	28	1.85
372139--372228	42	2.1	42	91	0	144	42	15	13	28	1.85
372274--372447	21	8.3	21	78	4	147	29	14	18	37	1.91
372274--372413	42	3.4	41	86	1	190	29	12	19	38	1.89
372274--372434	63	2.6	62	80	3	171	27	14	19	37	1.91
372274--372436	42	3.9	41	84	2	166	28	14	19	37	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
372513--372583	21	3.4	21	83	11	92	36	19	18	25	1.94
401787--401844	2	29.0	2	100	0	116	0	50	0	50	1.00
403036--403074	18	2.2	17	86	9	51	74	0	5	20	1.01
405822--405847	13	2.0	13	100	0	52	46	7	15	30	1.74
428990--429053	20	3.2	20	86	4	76	25	15	42	17	1.88
429010--429180	32	5.5	30	71	15	105	27	16	42	13	1.85
429049--429139	23	4.2	22	72	13	82	25	18	39	16	1.91
429060--429141	42	1.9	43	87	2	121	24	17	42	15	1.88
429125--429185	10	5.9	10	71	5	50	34	11	44	9	1.74
432910--432939	13	2.3	13	100	0	60	6	6	0	86	0.70

Tables:   1   2   3   4   5