genome.fa.s500.2.7.7.80.10.50.1000.4.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  4  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)
499464--499568	52	2.0	52	98	0	201	40	14	17	27	1.88
499766--499802	19	1.9	19	88	0	56	45	0	2	51	1.15
509606--509641	16	2.2	16	95	0	63	44	0	2	52	1.15
510342--510386	21	2.1	21	84	8	56	42	2	13	42	1.56
511493--511540	18	2.4	21	80	13	66	62	0	0	37	0.95
512155--512215	22	2.8	22	80	12	63	65	6	0	27	1.17
512713--512748	2	18.0	2	94	0	63	0	47	0	52	1.00
513539--513616	22	3.4	23	76	18	74	50	0	0	50	1.00
513555--513596	18	2.2	18	87	12	57	45	0	0	54	0.99
513564--513606	21	2.1	20	83	12	52	46	0	0	53	1.00
514149--514190	21	1.9	23	85	9	61	52	2	4	40	1.35
521119--521171	27	1.9	28	84	3	72	39	1	1	56	1.21
525559--526168	157	3.9	157	100	0	1220	39	21	12	26	1.89
527407--527449	22	2.0	22	86	9	61	60	0	0	39	0.97
528453--528478	13	2.0	13	100	0	52	61	0	0	38	0.96
528434--528477	20	2.1	21	88	12	65	59	0	0	40	0.98
528483--528526	18	2.6	16	80	13	52	56	0	0	43	0.99
528464--528517	22	2.5	22	79	5	58	51	0	0	48	1.00
528525--528550	6	4.3	6	100	0	52	53	0	0	46	1.00
529095--529134	21	1.9	21	85	10	55	50	0	0	50	1.00
529941--529979	19	2.0	20	85	5	53	43	0	0	56	0.99
529929--529987	31	1.9	31	86	13	86	38	0	0	61	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
529938--529995	21	2.8	21	75	19	59	39	0	0	60	0.97
529919--529989	36	2.0	35	83	8	90	39	0	0	60	0.97
530408--530470	21	3.5	17	80	16	56	68	0	0	31	0.90
531577--531676	36	2.8	36	76	19	109	51	4	1	44	1.27
532128--532226	45	2.2	46	87	1	146	41	3	6	49	1.43
533849--533884	12	3.0	12	91	0	63	72	0	27	0	0.85
536719--536751	16	2.0	17	94	5	59	36	0	0	63	0.95
537814--537841	2	14.0	2	100	0	56	50	0	0	50	1.00
538047--538081	18	1.9	18	94	0	61	37	0	5	57	1.23
538204--538243	16	2.5	16	79	0	53	35	2	0	62	1.09
538776--538815	18	2.4	16	83	8	53	52	0	0	47	1.00
539292--539327	18	1.9	19	88	5	56	50	0	0	50	1.00
539294--539371	28	2.9	28	70	14	74	53	0	0	46	1.00
539799--539832	2	17.0	2	100	0	68	50	0	0	50	1.00
541519--541553	2	18.0	2	94	5	63	0	51	0	48	1.00
542172--542208	18	2.0	19	89	5	58	51	2	0	45	1.15
542164--542230	21	3.6	18	75	21	59	52	1	0	46	1.09
542170--542262	27	3.4	27	80	12	84	53	1	0	45	1.07
542934--543015	5	15.8	5	70	16	51	47	0	0	52	1.00
542932--542988	27	2.1	28	86	3	80	49	0	0	50	1.00
542984--543035	24	2.2	24	82	6	61	48	0	0	51	1.00
542947--543041	39	2.5	38	76	15	99	49	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
543005--543044	19	2.1	19	85	0	53	47	0	0	52	1.00
543037--543074	20	1.9	20	89	10	60	52	0	0	47	1.00
543889--543914	2	13.0	2	100	0	52	50	0	0	50	1.00
545841--545867	2	13.5	2	100	0	54	51	0	0	48	1.00
545929--545970	15	2.7	16	82	13	52	50	0	2	47	1.14
555565--555599	16	2.2	16	90	10	54	68	0	0	31	0.90
565896--565939	2	22.5	2	95	4	81	52	0	0	47	1.00
573667--573698	15	2.1	16	94	5	57	21	0	0	78	0.76
573694--573768	10	7.7	10	77	14	59	44	1	0	54	1.08
573694--573756	29	2.2	27	83	8	72	46	0	0	53	1.00
573725--573759	14	2.5	14	90	0	52	42	0	0	57	0.99
575333--575374	18	2.4	19	88	11	63	38	0	0	61	0.96
575638--575689	16	3.1	16	75	8	50	38	1	3	55	1.29
581331--581357	14	1.9	14	100	0	54	0	7	0	92	0.38
585466--585557	37	2.3	41	85	7	129	52	0	0	47	1.00
585470--585561	12	6.9	15	68	26	57	52	0	0	47	1.00
585467--585562	42	2.3	41	82	12	108	52	0	0	47	1.00
585484--585570	5	17.2	5	69	15	54	47	0	0	52	1.00
586049--586087	19	2.1	19	100	0	78	38	5	10	46	1.60
591832--591899	10	7.2	10	75	15	65	70	1	1	26	1.04
591828--591878	21	2.3	22	83	16	70	70	1	1	25	1.08
591827--591922	39	2.4	39	77	13	99	64	2	3	30	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
593773--593821	2	24.5	2	100	0	98	48	0	0	51	1.00
596371--596403	16	2.1	16	88	11	50	57	0	0	42	0.98
596634--596690	29	1.9	30	82	10	73	47	5	5	42	1.48
596851--596894	2	22.0	2	100	0	88	50	0	0	50	1.00
598204--598245	9	4.5	10	80	14	54	69	0	0	30	0.89
600053--600088	2	18.0	2	88	0	54	50	0	2	47	1.15
602202--602240	16	2.4	17	83	16	55	58	2	0	38	1.12
602670--602724	2	27.5	2	96	0	101	50	1	0	47	1.11
604313--604348	19	1.9	18	88	5	54	63	0	0	36	0.94
604303--604350	23	2.0	23	84	11	62	64	0	0	35	0.94
604317--604355	19	2.1	19	85	0	51	64	0	0	35	0.94
609164--609191	2	14.0	2	100	0	56	50	0	0	50	1.00
614292--614333	22	2.0	21	90	4	66	50	0	0	50	1.00
615070--615122	23	2.3	23	81	9	65	37	0	0	62	0.96
616436--616467	2	16.0	2	100	0	64	50	0	0	50	1.00
617475--617528	25	2.1	26	83	10	67	61	3	0	35	1.14
622387--622468	40	2.1	40	88	2	121	26	19	24	29	1.98
629295--629343	19	2.8	17	78	9	55	46	0	0	53	1.00
629947--630007	2	30.5	2	77	6	61	49	0	1	49	1.10
629952--630031	31	2.5	33	82	13	105	51	0	2	46	1.14
633128--633169	21	2.0	20	86	4	57	33	9	52	4	1.55
635588--635653	30	2.2	30	97	2	125	33	25	6	34	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
643397--643434	5	7.6	5	82	11	51	36	0	0	63	0.95
643392--643437	19	2.3	21	85	7	69	39	0	0	60	0.97
660909--660956	19	2.5	19	78	18	55	66	0	2	31	1.03
661255--661294	18	2.2	19	90	4	64	72	0	2	25	0.97
661321--661365	21	2.1	21	95	0	81	46	20	11	22	1.81
662643--662700	29	2.0	29	96	0	107	53	31	1	13	1.50
669793--669827	18	1.9	18	88	11	54	34	0	0	65	0.93
670666--670717	2	26.5	2	84	3	61	40	0	5	53	1.25
674891--674930	19	2.1	19	86	9	55	42	2	0	55	1.13
676529--676617	19	4.6	19	71	19	69	39	1	1	58	1.13
676596--676625	11	2.7	11	89	0	51	40	0	0	60	0.97
677470--677533	36	1.9	32	84	15	85	48	0	1	50	1.10
678317--678346	15	2.0	15	100	0	60	40	0	0	60	0.97
678688--678717	2	15.0	2	100	0	60	50	0	0	50	1.00
679073--679101	2	14.5	2	100	0	58	0	48	0	51	1.00
687111--687162	26	2.0	26	92	0	86	25	11	15	48	1.78
689786--689815	3	10.0	3	100	0	60	66	0	0	33	0.92
690917--690987	11	6.8	11	71	16	62	67	0	0	32	0.91
690906--690979	20	3.7	20	78	10	62	66	0	0	33	0.92
690902--690969	33	2.1	34	88	5	104	67	0	0	32	0.91
690900--690971	32	2.2	32	85	9	101	65	0	0	34	0.93
690904--690991	22	4.4	20	76	18	78	65	0	0	34	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
690917--690996	20	3.8	20	75	9	72	66	0	0	33	0.92
690941--691001	24	2.7	22	76	11	70	60	0	0	39	0.97
691966--692037	19	3.6	19	85	12	83	38	0	0	61	0.96
691963--692039	20	3.7	22	83	10	92	40	0	0	59	0.97
702524--702551	2	14.0	2	100	0	56	50	0	0	50	1.00
703476--703513	13	2.7	14	88	8	51	50	2	5	42	1.39
705101--705165	17	3.9	16	78	7	67	49	1	0	49	1.10
705094--705168	17	4.0	18	71	23	57	49	1	0	49	1.09
705143--705220	28	2.7	29	76	11	81	56	1	1	41	1.15
705290--705329	3	13.3	3	100	0	80	32	0	0	67	0.91

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