oyster.v9_M.fa.s52.2.7.7.80.10.50.500.2.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: scaffold149
Parameters: 2 7 7 80 10 50 500
Length:  1065560

Tables:   1   2   3   4   

This is table  2  of  4  ( 442 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)
387415--387448	15	2.3	15	94	0	59	41	29	8	20	1.82
390114--390138	11	2.3	11	100	0	50	84	0	0	16	0.63
392179--392343	75	2.2	74	90	2	258	41	7	27	23	1.81
392319--392349	2	15.5	2	100	0	62	51	0	48	0	1.00
393542--393595	2	28.0	2	81	7	67	44	55	0	0	0.99
395950--395983	17	2.0	17	88	0	50	52	0	0	47	1.00
398073--398144	4	18.0	4	100	0	144	25	25	0	50	1.50
400435--400472	2	19.0	2	100	0	76	0	50	0	50	1.00
404556--404836	141	2.0	140	100	0	553	34	16	14	34	1.89
404910--404941	11	2.9	11	95	0	55	28	28	9	34	1.88
415747--415812	11	6.0	11	80	0	69	13	33	27	25	1.94
415749--415808	22	2.7	22	89	0	93	13	31	30	25	1.93
417028--417111	11	7.6	11	73	0	69	16	30	28	23	1.96
417028--417107	22	3.6	22	89	0	115	16	32	27	23	1.96
420728--420796	4	17.2	4	100	0	138	24	24	0	50	1.49
434822--434856	16	2.2	16	100	0	70	37	5	20	37	1.76
435480--435514	12	2.9	12	86	0	52	0	37	17	45	1.48
438551--438592	2	21.0	2	100	0	84	0	50	0	50	1.00
461852--461910	2	29.5	2	96	0	109	0	52	0	47	1.00
472870--472906	16	2.3	16	100	0	74	0	0	5	94	0.30
472870--472906	1	37.0	1	88	0	56	0	0	5	94	0.30
479540--479619	29	2.8	29	98	0	151	51	13	20	15	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
488401--488425	2	12.5	2	100	0	50	52	0	0	48	1.00
488584--488663	40	2.1	39	90	4	126	42	11	8	37	1.72
494473--494506	4	8.5	4	100	0	68	0	23	50	26	1.50
497551--498174	40	15.4	40	79	6	489	21	26	19	32	1.97
497551--498174	80	7.7	80	79	7	561	21	26	19	32	1.97
497993--498185	41	4.7	41	83	3	255	18	27	20	33	1.96
497551--498174	123	5.1	119	80	6	519	21	26	19	32	1.97
497964--498201	82	2.9	82	82	3	275	19	24	21	34	1.96
499033--499063	8	3.8	8	91	8	53	22	0	12	64	1.27
499036--499065	9	3.4	9	90	9	53	23	0	10	66	1.21
499033--499065	17	1.9	17	100	0	66	24	0	12	63	1.28
502215--502271	2	28.5	2	96	0	105	49	0	50	0	1.00
505553--505600	2	24.0	2	100	0	96	50	0	50	0	1.00
516797--516832	11	3.1	11	92	8	54	11	0	2	86	0.68
519526--519729	65	3.1	66	86	7	277	43	13	13	29	1.82
522285--522323	4	9.8	4	94	0	60	43	25	30	0	1.55
522284--522336	12	4.4	12	85	0	61	37	24	37	0	1.56
522284--522335	8	6.5	8	84	0	59	38	25	36	0	1.56
525582--525617	2	18.0	2	100	0	72	50	0	50	0	1.00
528620--528652	2	16.5	2	100	0	66	51	0	48	0	1.00
530379--530496	2	60.0	2	94	3	159	43	50	0	5	1.26
530496--530540	2	22.5	2	100	0	90	0	51	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
533305--533340	16	2.2	16	90	0	54	25	16	27	30	1.97
534040--534089	16	3.0	17	88	2	66	34	16	32	18	1.92
534137--534186	15	3.1	15	85	8	55	28	22	28	22	1.99
535000--535065	21	3.1	21	82	8	89	24	24	33	18	1.97
537242--537774	159	3.3	158	80	11	625	33	17	16	33	1.92
537170--537862	326	2.1	325	80	9	751	32	18	17	31	1.94
539844--539877	13	2.5	13	95	4	59	5	29	0	64	1.17
540923--540963	17	2.3	18	87	4	57	56	19	2	21	1.54
550632--550911	148	1.9	144	85	6	380	39	12	16	31	1.85
554729--555065	186	1.8	187	88	3	518	34	16	13	36	1.87
555664--555731	4	16.8	4	90	3	109	25	23	0	51	1.48
556101--556223	4	31.8	4	88	6	173	26	26	3	44	1.69
567996--568041	20	2.3	20	81	7	58	52	13	10	23	1.71
568934--568992	2	29.5	2	100	0	118	50	0	49	0	1.00
570444--570476	16	2.1	16	94	0	57	30	12	33	24	1.91
571402--571437	2	18.0	2	94	0	63	52	47	0	0	1.00
572988--573033	2	23.0	2	100	0	92	50	50	0	0	1.00
574365--574416	2	26.0	2	96	0	95	48	1	50	0	1.12
576184--576436	62	4.0	62	79	9	298	41	16	13	28	1.86
576184--576412	127	1.8	127	89	0	359	43	17	13	26	1.85
582005--582035	2	15.5	2	100	0	62	0	51	0	48	1.00
584298--584332	2	17.5	2	100	0	70	0	51	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
587342--587393	2	26.0	2	100	0	104	0	50	0	50	1.00
588106--588155	2	25.0	2	100	0	100	50	0	50	0	1.00
601123--601157	2	17.5	2	100	0	70	48	0	51	0	1.00
608526--608566	4	10.2	4	94	0	73	24	2	0	73	0.96
616011--616035	8	3.1	8	100	0	50	24	40	12	24	1.88
620031--620086	26	2.2	26	86	0	76	51	7	12	28	1.65
620037--620089	26	2.0	26	92	0	88	50	3	13	32	1.59
635448--635504	2	28.5	2	100	0	114	0	50	0	49	1.00
636524--636575	18	2.9	18	91	2	79	36	9	13	40	1.77
636747--636787	4	10.2	4	100	0	82	51	0	24	24	1.49
645167--645192	1	26.0	1	100	0	52	0	0	100	0	0.00
645270--645465	98	2.0	98	100	0	392	28	22	16	32	1.95
649216--649652	185	2.4	185	96	0	786	36	14	11	37	1.83
659988--660029	21	2.0	21	86	9	59	40	7	7	45	1.59
662347--662395	2	24.5	2	100	0	98	51	0	48	0	1.00
669028--669054	13	2.1	13	100	0	54	22	22	18	37	1.95
671511--671574	2	33.0	2	84	6	87	48	0	51	0	1.00
677734--677771	19	1.9	20	89	5	60	44	7	0	47	1.32
686229--686846	166	3.7	167	84	7	761	26	24	14	33	1.94
687003--687056	4	13.8	4	83	11	67	46	25	25	1	1.63
688732--689183	232	2.0	230	94	0	796	34	12	15	36	1.86
695709--695757	2	24.5	2	100	0	98	0	51	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
697031--697265	17	14.1	17	86	4	327	28	0	41	29	1.60
697124--697265	46	3.0	47	88	6	214	28	0	42	28	1.56
697105--697265	63	2.5	63	88	5	232	27	0	43	28	1.55
699836--699964	53	2.4	53	100	0	258	14	13	27	43	1.84
700091--700303	46	4.6	46	92	0	264	36	11	31	19	1.88
700899--701009	30	3.7	30	79	8	111	21	7	21	49	1.73
701626--701693	34	2.0	34	100	0	136	47	5	14	32	1.69
704410--704999	60	9.8	60	95	1	1072	31	20	8	39	1.82
704410--704999	182	3.3	181	95	1	1067	31	20	8	39	1.82
704410--704999	122	4.9	120	97	0	1072	31	20	8	39	1.82
706577--706686	36	3.1	36	98	0	211	46	14	16	22	1.83
709350--709397	2	24.0	2	100	0	96	0	50	0	50	1.00
709920--710253	39	8.6	39	87	3	487	23	7	23	45	1.78
710021--710081	18	3.2	18	67	13	50	21	8	27	42	1.81
709920--710251	156	2.1	156	99	0	655	23	7	23	45	1.78
711059--711336	47	6.2	47	78	10	303	30	14	16	38	1.88
711155--711232	38	2.1	38	90	0	120	29	16	11	42	1.83
711108--711333	85	2.6	86	86	6	294	30	14	15	39	1.88
713104--713266	13	12.5	13	75	5	132	20	6	39	33	1.79
713243--713415	76	2.3	76	94	2	303	18	16	32	32	1.93
713319--713343	13	1.9	13	100	0	50	16	0	44	40	1.47
713395--713432	13	2.9	13	92	0	67	15	0	42	42	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
714441--714613	55	3.1	55	91	2	256	31	13	23	31	1.93
716211--716252	14	3.1	14	93	3	68	26	21	23	28	1.99
721261--721315	26	2.1	26	100	0	110	30	12	29	27	1.93
724482--724540	2	30.5	2	89	6	95	0	49	0	50	1.00
725760--725801	17	2.3	18	84	15	52	45	0	47	7	1.30
725759--725801	19	2.2	20	80	19	56	46	0	46	6	1.30
728686--728757	23	3.2	22	62	14	56	36	12	23	27	1.91
728350--728811	46	10.0	46	97	0	861	28	16	24	30	1.97
729220--729287	21	3.5	19	77	14	68	54	0	0	45	0.99
729220--729290	16	4.7	15	77	19	60	54	0	0	45	0.99

Tables:   1   2   3   4