genome.fa.s500.2.7.7.80.10.50.1000.3.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: Scaffold500
Parameters: 2 7 7 80 10 50 1000
Length:  2046043

Tables:   1   2   3   4   5   6   7   8   9   10   

This is table  3  of  10  ( 1137 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)
317792--317834	12	3.3	13	87	9	61	37	0	0	62	0.95
317792--317863	25	2.9	25	84	12	78	37	0	1	61	1.05
317816--317873	26	2.3	24	78	18	64	43	0	1	55	1.10
318803--318898	45	2.1	45	92	0	156	56	13	0	30	1.38
318815--318885	22	3.2	22	65	11	54	53	16	0	29	1.44
319047--319114	6	11.7	6	80	12	61	48	29	16	5	1.69
320851--320915	27	2.4	28	87	10	98	24	6	23	46	1.75
326667--326699	16	2.1	16	100	0	66	36	6	24	33	1.80
329968--330021	20	2.7	20	85	8	65	59	3	3	33	1.33
329968--330035	19	3.4	21	80	11	63	60	5	2	30	1.35
333080--333185	55	1.9	55	80	0	122	36	1	15	46	1.57
333164--333216	25	2.1	25	82	6	63	13	1	20	64	1.38
333331--333635	102	3.0	102	99	0	592	34	4	21	39	1.75
333876--333949	33	2.4	30	86	8	96	31	8	24	36	1.84
335607--335696	21	4.1	21	84	4	99	56	8	21	13	1.64
337707--337751	16	2.9	15	81	12	54	53	0	0	46	1.00
337705--337760	24	2.5	22	77	13	60	55	1	0	42	1.10
341526--341563	19	2.0	19	100	0	76	5	21	10	63	1.46
347725--347817	2	46.5	2	82	4	116	4	2	43	50	1.34
347817--347845	2	14.5	2	100	0	58	48	0	0	51	1.00
359329--359382	23	2.3	23	87	6	74	27	1	3	66	1.19
363136--363187	17	3.3	15	80	17	52	34	1	1	61	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
364178--364214	15	2.6	14	91	4	56	59	0	0	40	0.97
366619--366648	11	2.7	11	94	0	51	43	6	3	46	1.46
373774--373812	15	2.5	15	87	4	51	53	0	0	46	1.00
373841--373882	17	2.5	17	84	0	57	47	2	0	50	1.14
378078--378105	2	14.0	2	100	0	56	50	0	0	50	1.00
378159--378199	2	20.5	2	100	0	82	51	0	0	48	1.00
380421--380467	21	2.4	20	86	10	62	38	0	0	61	0.96
384663--384706	23	1.9	23	90	0	70	52	18	6	22	1.69
389358--389392	18	1.9	18	94	0	61	51	0	0	48	1.00
389933--389964	16	1.9	17	93	6	57	90	0	9	0	0.45
389933--389966	6	6.0	6	93	6	54	88	0	11	0	0.52
391144--391206	32	2.0	32	87	3	92	49	0	0	50	1.00
391167--391214	17	2.9	16	79	17	53	52	0	0	47	1.00
391219--391255	18	2.0	18	94	5	65	64	0	0	35	0.94
396320--396375	29	1.9	29	82	7	69	53	0	5	41	1.24
397217--397255	19	1.9	19	85	10	51	53	0	2	43	1.14
397220--397269	21	2.5	20	84	15	59	52	0	2	46	1.12
397582--397634	21	2.6	19	79	11	52	54	0	3	41	1.18
398541--398593	15	3.7	15	80	5	56	43	1	1	52	1.23
402902--402961	11	5.5	11	75	18	54	60	0	0	40	0.97
402914--402959	20	2.2	22	88	7	69	60	0	0	39	0.97
402944--403006	33	1.9	33	84	12	85	47	1	1	49	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
402927--403029	29	3.4	28	70	18	73	55	0	0	42	1.13
403649--403707	26	2.4	25	78	15	70	49	0	1	49	1.11
404831--404872	2	21.5	2	95	4	77	0	47	0	52	1.00
412656--412744	31	2.9	31	73	14	78	55	2	0	42	1.12
412816--412857	16	2.7	16	81	3	59	40	2	0	57	1.12
413724--413794	36	1.9	36	83	11	90	54	0	0	45	0.99
414769--414794	7	3.7	7	100	0	52	15	0	0	84	0.62
415054--415121	34	2.0	34	88	8	104	47	0	0	52	1.00
415060--415130	33	2.2	33	82	10	83	52	0	0	47	1.00
416178--416250	21	3.6	19	77	15	58	39	1	4	54	1.28
419945--420037	46	2.0	46	100	0	186	34	21	12	31	1.91
423167--423204	2	19.5	2	94	5	69	50	0	50	0	1.00
424379--424430	22	2.3	24	84	12	67	51	0	5	42	1.25
424398--424447	22	2.3	22	85	0	64	52	0	4	44	1.20
425961--426006	21	2.2	21	96	0	83	47	8	32	10	1.69
429612--429647	2	18.0	2	100	0	72	50	0	0	50	1.00
432056--432120	32	2.0	32	82	11	80	58	1	0	40	1.07
434565--434605	16	2.6	16	85	11	57	36	2	2	58	1.24
435162--435195	2	17.5	2	93	6	61	50	0	0	50	1.00
436852--436904	20	2.6	19	74	14	52	50	1	9	37	1.46
437407--437457	21	2.4	21	75	18	52	62	1	9	25	1.36
440016--440063	14	3.3	14	79	5	51	52	4	2	41	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
440522--440548	2	13.5	2	100	0	54	51	0	0	48	1.00
440589--440647	20	2.9	22	78	19	65	55	0	0	44	0.99
444665--444690	2	13.0	2	100	0	52	50	0	0	50	1.00
444641--444741	51	2.0	51	98	0	193	32	8	13	44	1.75
444716--444748	2	16.5	2	100	0	66	48	0	0	51	1.00
445824--445880	26	2.2	26	87	0	78	35	7	14	43	1.72
449787--449830	23	1.9	23	81	9	54	40	0	29	29	1.57
450342--450404	20	3.6	17	76	14	65	39	0	0	60	0.97
450343--450384	20	2.2	19	95	4	75	30	0	0	69	0.89
450348--450391	20	2.2	20	91	0	70	40	0	0	59	0.98
451207--451242	2	18.0	2	100	0	72	50	0	0	50	1.00
453560--453608	22	2.2	22	82	7	55	36	2	6	55	1.37
453838--453880	2	21.5	2	95	0	77	46	2	0	51	1.13
456072--456109	2	19.0	2	88	0	58	50	5	0	44	1.24
456516--456546	16	1.9	16	93	0	53	41	0	3	54	1.16
456604--456638	9	4.0	9	88	3	54	57	0	0	42	0.99
457505--457534	2	15.5	2	93	6	53	50	0	0	50	1.00
461178--461230	2	26.5	2	100	0	106	49	0	0	50	1.00
472561--472585	13	1.9	13	100	0	50	36	16	16	32	1.90
472654--472678	13	1.9	13	100	0	50	32	16	16	36	1.90
472632--472698	33	2.0	33	88	0	98	40	13	11	34	1.81
478379--478411	16	2.1	16	88	11	50	45	3	0	51	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
478929--478999	30	2.5	30	84	11	87	42	0	1	56	1.08
478951--479009	28	2.0	30	84	12	79	49	0	0	50	1.00
478996--479056	23	2.7	21	82	12	68	36	1	0	62	1.05
479439--479519	28	2.9	28	70	18	71	41	0	1	56	1.07
481481--481529	26	1.9	25	95	4	89	48	0	0	51	1.00
481937--481969	16	2.1	16	88	11	50	45	3	0	51	1.16
482167--482205	20	2.1	18	90	9	60	56	5	0	38	1.22
485484--485516	16	2.1	16	88	11	50	45	3	0	51	1.16
486034--486104	30	2.5	30	84	11	87	42	0	1	56	1.08
486056--486114	28	2.0	30	84	12	79	49	0	0	50	1.00
486101--486161	23	2.7	21	82	12	68	36	1	0	62	1.05
486544--486624	28	2.9	28	70	18	71	41	0	1	56	1.07
488566--488618	17	3.2	17	72	2	54	52	0	0	47	1.00
489062--489099	19	2.0	19	90	10	60	2	10	0	86	0.66
489238--489282	18	2.4	18	82	10	56	55	0	0	44	0.99
491167--491220	21	2.6	20	74	8	54	53	5	0	40	1.24
491502--491538	2	19.5	2	89	10	60	0	48	0	51	1.00
491538--491562	2	12.5	2	100	0	50	48	0	0	52	1.00
493180--493283	11	8.2	14	68	23	63	38	0	0	61	0.96
493158--493222	32	2.0	33	87	3	96	41	1	0	56	1.08
493154--493278	17	7.1	17	71	17	69	38	0	0	60	1.02
493153--493281	27	4.9	27	70	16	92	37	0	0	61	1.02
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
493957--493981	5	5.0	5	100	0	50	40	20	0	40	1.52
494138--494210	32	2.3	32	83	6	87	56	1	1	41	1.16
494221--494262	5	8.4	5	79	10	50	66	0	0	33	0.92
494206--494264	19	3.0	20	75	18	61	64	0	0	35	0.94
494220--494264	11	4.4	10	83	11	56	66	0	0	33	0.92
494138--494264	59	2.2	60	78	12	140	59	0	0	39	1.09
495939--495972	2	17.0	2	100	0	68	50	0	0	50	1.00
497060--497092	3	11.0	3	93	0	57	30	0	3	66	1.06
497386--497440	27	2.1	26	83	10	67	49	1	0	49	1.11
499468--499549	25	3.2	25	63	24	62	40	14	15	29	1.87

Tables:   1   2   3   4   5   6   7   8   9   10