oyster.v9_M.fa.s1.2.7.7.80.10.50.500.2.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: scaffold22
Parameters: 2 7 7 80 10 50 500
Length:  1964558

Tables:   1   2   3   4   5   6   

This is table  2  of  6  ( 655 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)
316795--316833	16	2.4	16	86	0	51	35	48	7	7	1.61
317437--317479	16	2.7	16	85	0	59	11	9	46	32	1.72
317697--317746	2	25.0	2	95	0	91	0	48	0	52	1.00
323041--323075	2	17.5	2	93	0	61	54	0	45	0	0.99
323346--323384	2	19.5	2	89	0	60	51	2	46	0	1.14
324395--324434	2	20.0	2	100	0	80	50	0	50	0	1.00
329042--329075	2	17.0	2	100	0	68	50	0	50	0	1.00
339225--339281	18	3.1	18	80	14	62	52	8	1	36	1.43
339494--339623	15	8.1	15	70	18	84	46	13	3	36	1.61
339486--339668	50	3.8	49	75	13	166	46	13	4	36	1.63
339466--339702	98	2.4	99	81	12	253	45	11	5	37	1.63
339580--339614	18	1.9	18	94	0	61	51	8	0	40	1.33
339539--339685	15	9.3	15	69	15	64	44	13	4	36	1.65
339661--339727	32	2.1	32	82	0	80	46	7	8	37	1.64
339928--339980	20	2.6	20	84	0	70	41	15	3	39	1.65
342760--342902	71	2.0	71	95	0	259	20	17	20	41	1.91
348018--348131	57	2.0	56	96	1	210	30	13	21	33	1.92
356233--356287	23	2.4	23	100	0	110	20	30	7	41	1.79
356233--356297	10	5.6	13	76	23	74	21	30	7	40	1.81
359829--360051	112	2.0	112	92	1	376	30	8	15	46	1.75
364071--364095	13	1.9	13	100	0	50	16	28	16	40	1.89
367738--368402	331	2.0	330	99	0	1303	42	20	8	28	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
368352--368926	287	2.0	286	97	0	1105	35	19	12	32	1.89
370375--370464	11	8.1	11	70	9	58	12	10	27	50	1.72
370639--370669	11	2.8	11	90	0	53	9	16	29	45	1.79
370677--370719	11	3.7	12	84	12	54	48	27	13	9	1.73
377550--377579	16	1.9	15	93	6	51	43	3	13	40	1.60
387530--387705	35	5.1	35	90	2	275	21	16	18	43	1.88
394539--394564	11	2.4	11	100	0	52	34	26	7	30	1.85
402231--402264	12	2.8	12	95	0	59	0	35	26	38	1.57
402269--403064	146	5.5	145	86	5	1001	29	19	20	30	1.97
402269--403064	286	2.8	287	84	7	1040	29	19	20	30	1.97
404127--404154	2	14.0	2	100	0	56	50	0	0	50	1.00
404458--404506	2	24.5	2	100	0	98	0	48	0	51	1.00
408871--408903	16	2.1	16	94	0	57	0	33	24	42	1.55
416143--416183	13	3.3	13	76	13	50	51	2	12	34	1.52
417560--417586	2	13.5	2	100	0	54	48	51	0	0	1.00
430502--430553	27	1.9	27	84	0	68	78	19	0	1	0.84
434607--434651	20	2.2	20	100	0	90	62	24	0	13	1.31
437416--437525	52	2.1	53	87	1	159	38	8	9	44	1.66
439219--439256	20	1.9	20	85	15	53	15	15	21	47	1.82
450511--450912	200	2.0	200	100	0	804	42	15	12	28	1.84
452548--452585	2	19.0	2	100	0	76	0	50	0	50	1.00
462497--462543	2	23.5	2	100	0	94	51	0	48	0	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
463658--463722	2	32.5	2	100	0	130	49	0	50	0	1.00
480038--480070	15	2.2	16	89	10	52	33	6	0	60	1.21
481205--481236	11	2.9	11	90	0	55	43	37	3	15	1.63
481728--481788	22	2.8	22	82	0	68	32	14	42	9	1.79
481753--481802	14	3.4	14	76	10	55	30	18	46	6	1.73
481745--481802	30	1.9	30	96	0	107	31	17	44	6	1.75
482129--482169	2	20.5	2	100	0	82	48	0	51	0	1.00
483095--483239	75	1.9	75	100	0	290	44	11	7	36	1.68
483109--483225	36	3.2	36	61	15	85	46	10	8	35	1.69
483982--484034	2	27.0	2	88	3	81	47	0	49	3	1.19
492351--492675	41	7.9	40	78	9	321	20	50	3	25	1.64
492343--492670	83	4.0	82	88	2	442	20	50	3	25	1.62
501626--501860	116	2.0	116	82	8	289	33	10	18	37	1.86
507168--507214	3	15.3	3	91	4	76	36	0	29	34	1.58
507375--507399	2	12.5	2	100	0	50	48	0	0	52	1.00
510765--510799	17	2.1	17	100	0	70	42	0	22	34	1.54
518801--518855	2	27.5	2	100	0	110	49	0	50	0	1.00
532136--532165	15	2.0	15	93	0	51	36	20	6	36	1.79
537552--537609	27	2.1	27	93	0	98	24	12	5	58	1.54
537607--537700	45	2.1	46	97	2	181	41	4	14	39	1.66
549599--549695	48	2.0	48	92	4	160	35	17	10	37	1.84
550594--550618	12	2.1	12	100	0	50	52	0	40	8	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
573025--573066	21	2.0	21	100	0	84	33	0	14	52	1.42
574544--574622	2	40.0	2	97	2	151	0	49	0	50	1.00
575008--575044	2	18.5	2	100	0	74	0	51	0	48	1.00
585422--585463	2	21.0	2	100	0	84	0	50	0	50	1.00
588521--588551	15	2.1	15	93	0	53	25	9	25	38	1.86
591609--592503	81	11.2	80	83	4	1047	39	16	20	23	1.92
591609--592508	160	5.6	160	91	2	1321	39	16	20	23	1.92
608757--608792	2	18.0	2	100	0	72	50	0	50	0	1.00
611499--612628	166	6.8	166	88	3	1535	27	23	16	33	1.95
611501--612628	334	3.4	331	88	3	1624	27	23	16	33	1.95
611501--612628	500	2.3	497	88	3	1640	27	23	16	33	1.95
612801--612826	3	8.7	3	100	0	52	34	34	30	0	1.58
620768--620793	13	2.0	13	100	0	52	23	23	15	38	1.92
631692--631932	4	60.2	4	99	0	437	48	0	26	24	1.52
632138--632171	17	2.0	17	88	0	50	14	26	2	55	1.53
633041--633069	11	2.6	11	100	0	58	75	0	0	24	0.80
637322--637369	18	2.6	18	90	6	69	12	0	83	4	0.79
637322--637369	19	2.5	19	93	3	78	12	0	83	4	0.79
642786--642825	11	3.7	11	86	3	55	35	10	30	25	1.88
644812--644865	11	4.9	11	95	0	99	29	9	33	27	1.88
644897--644925	11	2.6	11	100	0	58	31	10	31	27	1.90
644942--644982	11	3.7	11	80	0	55	21	26	9	41	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
644991--645022	11	2.9	11	95	0	55	34	9	28	28	1.88
645025--645066	21	2.0	21	95	0	75	23	21	14	40	1.90
645403--645427	13	1.9	13	100	0	50	32	16	4	48	1.64
647980--648065	42	2.0	42	93	6	147	29	20	12	36	1.90
657452--657482	3	10.3	3	100	0	62	32	0	35	32	1.58
664456--664485	11	2.6	12	94	5	53	33	6	0	60	1.23
669710--669838	21	6.1	21	84	1	168	37	12	18	31	1.88
669708--669836	43	3.0	44	87	3	174	36	12	18	32	1.88
670246--670333	21	4.2	20	77	8	77	31	17	13	37	1.88
672286--672370	44	1.9	44	95	0	152	54	9	10	25	1.65
672839--672939	21	4.8	21	73	9	89	29	15	15	38	1.89
672822--672939	63	1.9	62	82	5	148	33	14	16	35	1.90
680560--680598	3	13.0	3	88	0	51	33	25	5	35	1.78
688049--688078	13	2.3	13	100	0	60	6	6	73	13	1.24
688075--688113	1	39.0	1	100	0	78	0	0	100	0	0.00
690047--690101	2	27.5	2	100	0	110	49	0	50	0	1.00
702304--702432	64	2.0	63	93	1	222	32	14	16	36	1.89
727908--727944	8	4.6	8	86	0	56	37	24	37	0	1.56
727905--727944	12	3.3	12	92	0	71	40	25	35	0	1.56
728161--728185	9	2.8	9	100	0	50	72	0	8	20	1.10
744671--744790	40	3.0	40	100	0	240	40	22	5	32	1.76
744872--744899	14	2.0	14	100	0	56	35	14	0	50	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
746848--746895	2	24.0	2	100	0	96	50	0	50	0	1.00
752625--752649	13	1.9	13	100	0	50	32	0	24	44	1.54
753727--753798	32	2.2	33	87	5	110	43	4	11	41	1.59
758446--758489	2	22.0	2	100	0	88	0	0	50	50	1.00
762790--762897	54	2.0	54	94	0	189	33	12	16	37	1.87
763462--763500	17	2.2	19	90	9	64	33	7	20	38	1.81
766552--766594	3	14.3	3	95	0	77	30	0	2	67	1.03
767131--767159	3	9.7	3	100	0	58	34	0	0	65	0.93
767226--767268	3	14.3	3	95	0	77	30	0	2	67	1.03
767805--767833	3	9.7	3	100	0	58	34	0	0	65	0.93

Tables:   1   2   3   4   5   6