oyster.v9_M.fa.s10.2.7.7.80.10.50.500.2.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: scaffold77
Parameters: 2 7 7 80 10 50 500
Length:  1619719

Tables:   1   2   3   4   

This is table  2  of  4  ( 471 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)
387038--387132	48	2.0	47	97	0	172	38	14	15	29	1.88
388886--388951	21	3.1	20	70	8	51	27	15	25	31	1.95
389064--389692	21	30.0	21	75	6	407	25	25	23	26	2.00
389069--389696	42	15.0	42	75	5	475	24	25	23	26	2.00
389258--389678	212	2.0	212	84	0	556	25	25	23	25	2.00
389215--389701	212	2.3	210	82	2	553	25	25	23	26	2.00
389685--389724	21	1.9	21	84	0	53	30	25	17	27	1.97
391498--391522	10	2.5	10	100	0	50	48	12	28	12	1.76
406572--407568	179	5.6	179	88	1	1421	31	16	19	32	1.94
406577--407568	357	2.8	357	88	1	1483	31	16	19	32	1.94
415662--416510	164	5.3	162	75	9	609	36	18	16	28	1.93
417000--417046	2	23.5	2	95	0	85	0	0	51	48	1.00
417398--417436	19	2.1	19	95	0	69	33	15	15	35	1.89
418175--418200	3	8.7	3	100	0	52	69	0	30	0	0.89
419150--419174	10	2.5	10	100	0	50	12	28	12	48	1.76
422651--422924	64	4.3	63	80	0	242	25	24	25	24	2.00
422624--422929	64	4.8	64	80	1	233	25	25	24	24	2.00
422633--422924	85	3.5	84	80	3	309	25	24	25	24	2.00
422619--422936	21	15.0	21	77	3	289	26	24	24	24	2.00
422897--422942	21	2.2	21	88	0	65	26	28	23	21	1.99
428502--428532	15	2.1	15	93	0	53	38	3	0	58	1.15
464278--464321	4	11.0	4	85	0	52	2	40	25	31	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
464278--464325	12	4.0	12	91	0	78	2	39	25	33	1.67
464295--464333	4	9.8	4	88	0	51	0	33	25	41	1.56
464291--464334	8	5.5	8	83	0	61	0	36	25	38	1.56
468592--468644	21	2.5	21	87	0	70	43	22	11	22	1.85
470288--470547	21	12.3	21	78	5	238	26	24	25	24	2.00
470291--470521	63	3.7	63	82	4	270	25	24	26	24	2.00
499928--499960	2	16.5	2	100	0	66	51	0	48	0	1.00
527052--527650	38	15.8	38	92	1	997	21	23	15	40	1.90
534747--534781	14	2.5	14	85	0	52	51	8	0	40	1.33
541353--541434	27	3.0	27	94	0	146	28	26	9	35	1.88
556798--556844	2	23.5	2	100	0	94	0	48	0	51	1.00
561367--561415	25	2.0	25	87	0	71	46	2	12	38	1.53
569563--570873	166	7.9	166	83	5	1509	33	14	22	29	1.94
569564--570873	333	4.0	330	83	6	1518	33	14	22	29	1.94
569583--570873	499	2.6	495	83	6	1559	33	14	22	29	1.94
582681--582725	14	3.2	14	90	0	72	40	13	17	28	1.88
604300--605112	172	4.8	166	82	7	933	31	17	18	32	1.94
604300--605098	170	4.7	168	82	6	943	31	17	18	32	1.94
607981--608132	75	2.0	75	90	0	241	26	17	42	14	1.87
609674--609801	47	2.8	46	79	9	143	24	35	21	19	1.96
618862--619037	88	2.0	88	96	0	325	37	15	22	23	1.93
620640--621107	145	3.2	145	83	2	564	27	22	19	30	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
633838--633884	21	2.2	21	92	0	76	40	38	8	12	1.74
635771--635863	31	3.0	31	91	1	150	30	25	16	27	1.96
637117--637151	16	2.2	16	100	0	70	25	22	22	28	1.99
637117--637162	16	3.0	16	90	6	60	26	26	17	30	1.97
638433--638754	168	1.9	164	86	5	459	33	19	15	30	1.94
639559--639888	176	1.9	177	83	1	439	33	24	17	24	1.96
640236--640289	22	2.5	22	78	6	65	40	14	35	9	1.78
645663--645692	15	2.0	15	93	0	51	30	33	26	10	1.89
647234--647266	17	1.9	17	100	0	66	30	24	21	24	1.99
649887--649931	2	22.5	2	100	0	90	0	48	0	51	1.00
650544--650595	2	26.0	2	94	0	86	46	0	51	1	1.12
651125--651155	12	2.6	12	94	0	53	3	35	25	35	1.72
652140--652175	2	18.0	2	91	0	54	44	0	52	2	1.15
652704--652734	12	2.6	12	94	0	53	3	35	25	35	1.72
660229--661209	438	2.3	432	81	8	1077	28	16	16	38	1.90
662609--662990	164	2.3	165	86	4	529	29	22	12	34	1.92
663754--663805	17	3.1	17	81	13	63	38	13	19	28	1.89
666263--666299	19	1.9	19	88	0	56	40	32	5	21	1.76
667657--667690	15	2.3	15	89	0	50	41	14	5	38	1.70
669125--669150	12	2.2	12	100	0	52	23	7	15	53	1.67
669298--669367	29	2.4	29	85	0	95	44	14	20	21	1.86
671270--671611	168	2.0	166	80	4	375	29	19	19	31	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
672152--672200	17	3.1	16	80	11	55	26	20	10	42	1.84
681649--681692	16	2.8	16	96	0	79	15	50	25	9	1.74
681716--681755	21	1.9	21	89	0	62	35	35	20	10	1.86
683214--683267	19	2.8	19	74	0	63	37	16	22	24	1.94
683554--683591	19	2.0	19	94	0	67	31	23	15	28	1.96
686868--686913	4	11.5	4	85	0	56	6	45	19	28	1.75
687684--687723	21	1.9	21	94	0	71	42	10	20	27	1.83
687684--687723	11	3.7	11	86	6	64	42	10	20	27	1.83
687728--687759	11	2.9	11	95	0	55	28	28	9	34	1.88
687768--687808	11	3.7	11	80	0	55	41	9	26	21	1.84
687768--687820	22	2.4	22	87	0	79	41	11	26	20	1.86
687825--687853	11	2.6	11	100	0	58	27	31	10	31	1.90
687885--687938	11	4.9	11	95	0	99	27	33	9	29	1.88
688957--689179	112	2.0	112	96	0	410	30	18	19	31	1.96
689393--689459	2	33.5	2	100	0	134	50	0	49	0	1.00
689776--689836	22	2.8	22	78	9	70	42	14	24	18	1.88
689829--689879	11	4.7	11	92	2	77	35	9	27	27	1.88
689949--689988	11	3.7	11	90	3	55	25	30	10	35	1.88
690668--690767	4	25.2	4	94	2	175	25	25	0	50	1.50
700039--700105	7	9.6	7	83	0	89	35	14	22	26	1.93
704793--704819	4	6.8	4	100	0	54	0	25	22	51	1.48
704817--704852	2	18.0	2	94	0	63	2	50	0	47	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
736224--736255	2	16.0	2	100	0	64	50	0	0	50	1.00
739089--739208	17	7.1	17	93	0	186	14	19	12	54	1.71
747817--747841	13	1.9	13	100	0	50	8	24	20	48	1.76
750352--750407	2	28.0	2	92	0	94	0	50	0	50	1.00
764972--765149	87	2.0	87	86	2	250	36	17	14	31	1.90
780556--780609	19	2.8	19	80	0	72	35	14	24	25	1.94
784084--784121	13	3.0	13	88	3	51	78	0	0	21	0.74
784955--784989	18	1.9	18	88	0	52	88	5	0	5	0.63
784966--784992	10	2.7	10	100	0	54	88	11	0	0	0.50
785010--785039	1	30.0	1	93	0	51	0	96	0	3	0.21
785840--785871	16	2.0	16	93	0	55	25	9	0	65	1.22
785955--785989	2	17.5	2	100	0	70	0	51	0	48	1.00
786155--786201	20	2.4	20	82	7	60	61	6	10	21	1.50
787340--787364	13	1.9	13	100	0	50	0	96	0	4	0.24
787339--787365	14	1.9	14	100	0	54	0	96	0	3	0.23
787338--787366	15	1.9	15	100	0	58	0	96	0	3	0.22
791441--791465	13	1.9	13	100	0	50	32	0	24	44	1.54
792725--793051	166	2.0	165	90	2	523	33	17	14	33	1.90
803372--803400	15	1.9	15	100	0	58	37	13	13	34	1.85
804691--804788	39	2.4	41	83	6	121	36	15	8	39	1.77
807191--807217	10	2.7	10	100	0	54	7	59	11	22	1.56
807194--807259	31	2.1	31	83	5	80	10	42	15	31	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
807233--807315	42	1.9	43	85	4	114	14	43	16	25	1.86
807322--807366	20	2.2	20	88	0	63	13	44	15	26	1.83
807339--807385	20	2.4	20	85	7	60	12	42	17	27	1.85
808322--808374	2	26.5	2	100	0	106	49	0	50	0	1.00
808567--808613	2	23.5	2	100	0	94	51	0	48	0	1.00
808876--809158	141	2.0	136	85	6	372	28	20	22	27	1.99
809295--809354	11	5.9	10	71	9	50	35	11	43	10	1.75
812103--812133	9	3.4	9	100	0	62	45	9	25	19	1.81
818474--818515	2	21.0	2	100	0	84	50	0	50	0	1.00
820296--821226	437	2.1	437	90	1	1445	30	18	14	36	1.91

Tables:   1   2   3   4