genome.fa.s454.2.7.7.80.10.50.1000.3.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.09

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: Scaffold454
Parameters: 2 7 7 80 10 50 1000
Length:  526734

Tables:   1   2   3   4   

This is table  3  of  4  ( 420 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)
249312--249462	5	32.4	5	66	19	60	41	1	0	56	1.12
249312--249432	32	4.4	27	71	19	72	43	1	0	53	1.16
249361--249428	18	3.6	19	75	11	59	47	1	0	51	1.09
249354--249446	42	2.3	40	77	3	96	44	1	0	54	1.07
249376--249448	20	3.7	20	80	12	71	43	0	0	56	0.99
249606--249638	13	2.4	14	85	10	50	33	0	0	66	0.92
249720--249750	16	1.9	16	93	0	53	64	0	0	35	0.94
249871--249904	2	17.5	2	93	6	61	47	0	0	52	1.00
252916--252952	19	2.0	19	85	15	51	24	8	0	67	1.17
252938--252974	12	3.2	12	88	3	58	10	10	0	78	0.97
253954--253984	11	2.8	11	95	0	53	3	9	0	87	0.66
254079--254143	22	2.9	22	73	8	60	49	1	6	43	1.37
254118--254157	16	2.6	16	84	4	55	50	0	2	47	1.14
256945--256990	24	2.0	23	86	4	65	47	2	0	50	1.13
256970--256999	12	2.5	12	88	0	51	60	0	0	40	0.97
257032--257104	24	3.1	24	62	31	57	52	10	9	27	1.68
257010--257104	47	2.0	47	95	0	172	51	10	8	29	1.65
257901--257930	3	10.0	3	100	0	60	66	0	0	33	0.92
261251--261292	5	8.2	5	82	10	50	38	2	2	57	1.25
261321--261417	16	5.9	16	80	2	104	48	3	6	42	1.44
261340--261426	32	2.7	32	82	3	113	47	3	6	42	1.47
261529--261621	16	5.5	16	72	16	71	49	1	2	47	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
264041--264076	2	18.0	2	100	0	72	50	0	0	50	1.00
279865--279893	15	2.0	15	93	6	51	41	10	13	34	1.79
280044--281144	547	2.0	549	97	1	2073	32	15	14	37	1.88
283273--283334	31	2.0	32	87	9	92	30	0	0	69	0.89
284077--284117	21	2.0	21	90	9	66	58	0	0	41	0.98
285031--285072	22	2.0	22	86	13	61	33	0	4	61	1.17
293106--293149	20	2.2	20	83	0	52	40	0	0	59	0.98
294436--294504	35	1.9	36	83	13	90	68	2	1	27	1.13
294632--294657	2	13.0	2	100	0	52	50	0	0	50	1.00
303180--303236	26	2.2	26	78	15	64	54	0	1	43	1.10
303835--303879	6	7.5	6	89	0	63	46	4	2	46	1.35
303835--303879	10	4.5	10	88	0	63	46	4	2	46	1.35
303835--303879	4	11.2	4	85	0	63	46	4	2	46	1.35
305250--305332	2	43.0	2	72	15	50	49	4	3	42	1.41
305407--305455	2	26.0	2	78	12	50	46	2	4	46	1.33
305195--305618	127	3.4	126	80	5	509	36	5	9	48	1.58
306619--306654	2	18.0	2	88	0	54	55	44	0	0	0.99
309404--309434	2	15.5	2	100	0	62	51	0	0	48	1.00
309434--309459	2	13.0	2	100	0	52	50	0	50	0	1.00
309776--309818	2	21.5	2	100	0	86	51	0	0	48	1.00
313732--313762	2	15.5	2	100	0	62	48	0	51	0	1.00
316195--316256	6	10.0	6	74	6	52	43	1	0	54	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
316195--316259	25	2.6	25	90	2	94	43	1	0	55	1.09
316195--316250	12	4.5	12	88	6	85	41	1	0	57	1.09
316267--316297	7	4.4	7	91	0	53	80	0	0	19	0.71
317043--317067	4	6.2	4	100	0	50	52	24	24	0	1.48
318144--318170	2	13.5	2	100	0	54	51	0	0	48	1.00
319632--319676	22	2.0	22	87	12	65	68	0	0	31	0.89
319641--319682	22	1.9	22	85	9	59	71	2	0	26	0.98
319682--319762	32	2.6	32	73	13	78	43	0	0	56	0.99
322224--322258	6	5.8	6	93	0	61	0	2	82	14	0.77
322980--323005	12	2.2	12	100	0	52	34	30	0	34	1.58
326846--326926	16	5.1	16	75	14	69	41	24	13	19	1.88
326846--326926	32	2.5	32	84	4	92	41	24	13	19	1.88
328798--328854	29	2.0	28	82	3	69	31	17	28	22	1.97
328890--328963	28	2.6	28	87	4	96	31	18	25	24	1.98
328947--329115	51	3.3	51	81	8	209	33	11	23	30	1.91
336314--336353	17	2.4	17	95	0	71	30	10	30	30	1.90
336526--336595	20	3.5	19	86	7	95	41	14	15	28	1.86
336634--336690	13	4.8	13	74	24	63	40	10	15	33	1.82
336634--336712	33	2.4	33	100	0	140	41	10	15	32	1.80
336646--336710	20	3.6	20	69	26	72	43	7	15	33	1.75
342365--342394	2	15.5	2	93	6	53	46	0	0	53	1.00
347573--347626	17	3.1	19	76	17	62	42	0	0	57	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
352352--352405	24	2.2	24	83	3	63	50	0	0	50	1.00
354455--354507	25	2.1	25	82	6	63	49	0	3	47	1.19
354695--354727	2	16.5	2	100	0	66	51	0	0	48	1.00
355877--355916	2	20.0	2	100	0	80	50	0	0	50	1.00
357668--357715	2	24.0	2	86	0	69	50	6	0	43	1.27
358117--358167	24	2.2	23	89	3	75	62	1	5	29	1.29
361932--361957	2	13.0	2	100	0	52	50	0	0	50	1.00
364395--364427	2	17.0	2	93	6	59	48	0	0	51	1.00
365196--365337	74	1.9	73	88	4	214	40	10	25	23	1.87
367688--367720	2	16.5	2	93	0	57	48	0	51	0	1.00
377716--377741	1	26.0	1	100	0	52	0	0	100	0	0.00
381996--382054	14	4.2	14	85	6	66	47	1	0	50	1.11
383774--383871	36	3.0	34	77	11	98	28	26	13	31	1.94
387209--387309	51	2.0	52	90	2	159	42	12	16	27	1.85
387122--387298	91	1.9	92	88	1	266	42	11	15	29	1.82
388862--388900	20	2.0	20	90	10	62	12	28	0	58	1.34
390458--390519	31	2.0	31	87	9	92	32	19	9	38	1.84
390458--390553	35	2.9	32	79	13	99	33	20	9	36	1.85
391231--391270	20	1.9	21	85	10	55	35	10	7	47	1.65
392814--392924	24	4.6	24	75	4	98	28	6	6	58	1.47
395557--395607	26	2.0	26	84	7	68	47	3	1	47	1.32
398753--398882	66	2.0	66	95	0	233	27	15	19	37	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
402783--402817	2	18.5	2	88	11	56	54	0	0	45	0.99
406161--406197	19	2.0	19	89	5	58	70	0	2	27	1.01
406286--406344	16	3.7	16	86	6	75	33	0	8	57	1.29
406286--406352	32	2.1	30	79	15	73	32	0	7	59	1.25
406286--406352	16	4.3	15	83	7	64	32	0	7	59	1.25
406884--406912	3	9.7	3	100	0	58	31	0	0	68	0.89
413717--413741	9	2.8	9	100	0	50	36	0	0	64	0.94
414876--414911	2	18.5	2	94	5	65	47	0	0	52	1.00
415603--415630	3	9.3	3	100	0	56	64	0	0	35	0.94
416035--416060	2	13.0	2	100	0	52	50	0	0	50	1.00
416340--416414	22	3.4	22	75	15	66	52	1	0	46	1.09
421176--421212	12	3.2	12	82	17	51	64	0	0	35	0.94
421236--421286	15	3.1	15	81	15	57	35	0	0	64	0.94
421302--421360	26	2.3	27	85	14	88	28	0	0	71	0.87
421258--421336	16	4.6	17	72	17	58	27	3	0	68	1.07
421313--421360	15	3.5	15	72	16	50	29	0	0	70	0.87
421258--421360	52	2.0	50	81	11	118	29	2	0	67	1.05
434737--434765	6	4.8	6	100	0	58	17	17	31	34	1.93
435813--435854	15	2.8	15	78	10	50	47	0	4	47	1.23
435852--435897	23	2.0	23	100	0	92	21	4	8	65	1.38
435855--435907	23	2.3	23	90	3	79	22	5	7	64	1.41
435950--435975	2	13.0	2	100	0	52	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
437358--437510	48	3.4	45	74	21	126	60	2	1	35	1.22
437503--437550	19	2.5	19	86	10	62	60	2	0	37	1.09
438199--438247	22	2.3	20	86	10	62	55	2	0	42	1.11
438199--438248	20	2.3	20	80	10	55	56	2	0	42	1.11
438569--438594	4	6.5	4	100	0	52	53	0	0	46	1.00
440107--440871	396	2.0	386	93	2	1314	39	15	15	29	1.88
442171--442252	19	5.1	16	79	20	68	35	12	14	37	1.84
442191--442228	13	2.9	13	100	0	76	36	15	15	31	1.90
442290--442315	13	2.0	13	100	0	52	30	15	15	38	1.88
442270--442336	33	2.0	33	88	0	98	25	14	16	43	1.86

Tables:   1   2   3   4