genome.fa.s4.2.7.7.80.10.50.1000.2.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: Scaffold4
Parameters: 2 7 7 80 10 50 1000
Length:  5986281

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   

This is table  2  of  31  ( 3628 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)
362315--362342	14	2.0	14	100	0	56	57	0	0	42	0.99
365068--365096	3	9.7	3	100	0	58	68	0	0	31	0.89
365546--365596	2	26.0	2	88	4	77	49	0	50	0	1.00
371387--371440	22	2.5	22	84	6	65	27	12	35	24	1.92
371400--371452	22	2.4	22	83	3	61	32	13	33	20	1.91
372229--372265	2	18.0	2	88	5	56	45	0	5	48	1.25
372491--372562	34	2.1	34	82	10	85	34	1	4	59	1.25
372509--372563	17	3.3	16	76	16	58	29	1	5	63	1.27
372789--372997	102	2.0	102	89	3	321	33	15	18	33	1.92
375278--375333	3	18.7	3	96	0	103	64	1	0	33	1.04
375659--375688	2	15.0	2	100	0	60	50	0	0	50	1.00
376304--376329	13	2.0	13	100	0	52	30	0	7	61	1.24
376370--376400	15	2.0	15	93	6	53	19	0	0	80	0.71
376390--376422	15	2.1	16	88	5	50	45	0	0	54	0.99
376454--376485	16	2.0	16	93	0	55	46	0	0	53	1.00
376548--376612	14	4.8	14	70	12	55	49	0	0	50	1.00
376976--377045	32	2.2	33	79	7	81	45	0	2	51	1.16
377735--377777	18	2.4	18	92	3	70	60	0	0	39	0.97
378063--378099	17	2.1	18	90	5	58	51	0	0	48	1.00
378619--378660	13	3.2	13	77	16	50	57	2	0	40	1.12
389632--389746	56	2.1	54	90	3	176	39	15	15	29	1.89
392432--392456	13	1.9	13	100	0	50	0	0	8	92	0.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
393809--393846	2	19.0	2	100	0	76	50	0	0	50	1.00
396039--396079	17	2.4	16	84	11	55	41	0	7	51	1.30
400756--400803	24	2.0	24	95	0	87	45	10	12	31	1.76
400952--400992	21	2.0	21	85	4	57	51	2	0	46	1.14
402675--402712	2	19.0	2	94	0	67	50	0	2	47	1.15
405740--405783	19	2.5	19	82	14	58	45	0	0	54	0.99
413882--413930	16	3.1	16	85	5	64	48	0	0	51	1.00
413902--413948	22	2.1	22	88	0	67	51	0	2	46	1.13
413885--413982	37	2.6	37	79	6	99	46	2	2	48	1.25
414049--414101	18	2.8	18	76	17	54	43	0	0	56	0.99
415159--415213	3	18.3	3	92	0	92	67	3	0	29	1.08
417734--417764	2	15.5	2	100	0	62	0	48	0	51	1.00
417764--417804	2	21.0	2	85	5	57	43	0	0	56	0.99
418931--418960	16	1.9	16	93	6	53	0	13	0	86	0.57
420850--420894	19	2.4	19	88	7	65	46	0	0	53	1.00
420823--420893	16	3.9	18	75	15	67	43	0	0	56	0.99
420850--420893	21	2.2	21	88	11	67	47	0	0	52	1.00
424301--424336	3	12.0	3	100	0	72	33	0	0	66	0.92
424428--424471	2	22.0	2	100	0	88	50	0	0	50	1.00
425323--425374	16	3.2	16	86	0	68	51	26	5	15	1.65
425332--425382	16	3.2	16	85	0	66	54	31	3	9	1.51
429179--429230	27	1.9	27	84	7	70	40	1	1	55	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
432501--432550	17	2.9	17	77	13	57	38	0	2	60	1.09
433207--433239	2	16.5	2	100	0	66	51	0	0	48	1.00
434446--434475	3	9.7	3	92	7	51	63	0	3	33	1.11
436643--436677	2	17.5	2	100	0	70	51	0	0	48	1.00
437603--437675	27	2.7	27	84	0	101	31	6	15	46	1.71
439101--439191	27	3.5	27	73	5	80	31	7	16	43	1.76
452459--452525	28	2.4	27	78	14	82	52	1	0	46	1.09
452916--452989	15	5.0	15	74	9	71	35	13	10	40	1.80
454878--455062	95	1.9	96	94	1	327	40	13	23	22	1.90
456692--456728	2	18.5	2	94	0	65	51	0	48	0	1.00
461020--461061	15	2.9	15	82	3	50	35	0	0	64	0.94
465975--465999	2	12.5	2	100	0	50	0	48	0	52	1.00
466675--466716	14	3.1	14	83	10	52	64	0	0	35	0.94
466712--466811	25	3.9	26	81	13	102	58	2	0	40	1.10
477403--477598	97	2.0	97	100	0	392	44	13	18	23	1.85
484261--484358	39	2.5	39	86	4	128	21	16	25	36	1.94
484261--484369	39	2.8	38	82	9	114	22	16	25	35	1.94
488742--488779	15	2.4	16	91	8	69	23	0	0	76	0.79
512885--512927	22	2.0	21	81	4	50	60	0	2	37	1.10
512935--512973	13	3.2	12	89	7	53	56	0	0	43	0.99
513943--513994	22	2.5	22	87	6	72	42	1	0	55	1.10
514713--514754	22	1.9	22	85	9	59	61	2	0	35	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
515132--515179	20	2.3	22	85	7	64	50	0	4	45	1.21
518713--518770	19	3.2	18	79	13	66	60	0	0	39	0.97
518815--518859	24	1.9	23	86	4	63	53	0	0	46	1.00
529933--530018	43	2.0	43	100	0	172	32	11	20	34	1.89
533649--533707	3	19.7	3	96	0	109	66	0	33	0	0.92
536662--536690	2	14.5	2	100	0	58	51	0	0	48	1.00
536999--537028	2	15.0	2	100	0	60	50	0	0	50	1.00
539369--539460	37	2.6	37	86	8	131	63	4	10	21	1.44
541552--541578	2	13.5	2	100	0	54	51	0	0	48	1.00
542885--542918	16	2.1	16	89	10	52	44	0	0	55	0.99
543071--543124	21	2.4	22	81	9	56	40	1	0	57	1.09
543724--543750	2	13.5	2	100	0	54	48	0	0	51	1.00
546918--546942	2	12.5	2	100	0	50	52	0	48	0	1.00
551354--551393	3	13.3	3	100	0	80	35	0	0	65	0.93
557253--557284	2	16.0	2	100	0	64	50	0	0	50	1.00
559008--559040	2	16.5	2	100	0	66	0	48	0	51	1.00
562911--562941	2	15.5	2	93	0	53	45	0	3	51	1.17
562947--562978	3	10.7	3	100	0	64	31	34	0	34	1.58
566647--566675	15	2.0	15	93	6	51	27	24	27	20	1.99
567231--567264	2	17.0	2	100	0	68	50	0	0	50	1.00
568189--568247	19	3.3	19	75	18	63	61	0	0	38	0.96
568236--568283	20	2.5	20	83	12	64	68	0	6	25	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
568424--568448	5	5.0	5	100	0	50	40	20	40	0	1.52
576148--576386	118	2.0	118	95	0	433	37	19	20	23	1.94
578554--578591	2	19.0	2	100	0	76	50	0	0	50	1.00
579998--580037	3	13.3	3	100	0	80	67	0	0	32	0.91
587740--587785	16	2.8	16	80	3	56	47	2	2	47	1.26
587776--587815	14	2.9	14	80	0	53	50	0	0	50	1.00
587758--587834	38	2.0	39	82	10	95	46	1	2	49	1.23
589430--589505	33	2.2	36	83	6	95	44	1	1	52	1.17
600190--600739	282	2.0	279	85	6	745	28	14	20	36	1.92
600462--601652	407	3.0	390	84	5	1530	29	15	21	33	1.94
603111--603155	22	2.2	20	88	8	63	62	0	2	35	1.08
627941--628017	28	3.0	24	74	17	75	41	0	3	54	1.19
629267--629298	2	15.5	2	93	6	55	46	3	0	50	1.17
630815--630894	34	2.4	34	86	0	106	38	2	13	45	1.58
634990--635040	26	1.9	28	84	11	72	52	7	0	39	1.30
634990--635054	26	2.5	25	80	12	60	56	7	0	35	1.28
637915--637956	21	2.1	19	86	8	57	40	2	0	57	1.12
640238--640276	16	2.5	16	83	4	53	51	0	0	48	1.00
640238--640327	16	6.3	15	67	25	52	53	0	2	44	1.13
642094--642120	2	13.5	2	100	0	54	48	0	0	51	1.00
649008--649106	51	1.9	52	86	10	141	47	0	2	50	1.12
649400--649448	20	2.3	21	82	6	64	48	0	2	48	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
649401--649459	22	2.7	21	82	10	57	45	0	3	50	1.18
653066--653149	39	2.2	39	88	0	123	29	10	16	42	1.82
655182--655277	48	2.0	48	97	0	183	44	10	20	23	1.82
658066--658092	6	4.5	6	100	0	54	18	18	29	33	1.95
659038--659072	3	11.7	3	100	0	70	68	0	0	31	0.90
660277--660341	19	3.3	19	72	12	51	46	0	0	53	1.00
660885--660951	23	2.7	24	77	11	73	58	1	2	37	1.23
660944--661030	32	2.7	33	77	13	94	49	0	2	48	1.13
660957--661054	32	3.2	30	75	15	76	54	0	1	44	1.07
660981--661054	36	2.0	38	84	5	98	58	0	0	41	0.98

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31