genome.fa.s1.2.7.7.80.10.50.1000.24.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: Scaffold1
Parameters: 2 7 7 80 10 50 1000
Length:  8764944

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   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   

This is table  24  of  52  ( 6211 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)
3952085--3952153	35	2.0	35	97	0	129	57	10	14	17	1.63
3953232--3953277	3	15.3	3	100	0	92	32	0	0	67	0.91
3955582--3955611	9	3.2	9	95	4	51	86	0	10	3	0.67
3955995--3956047	17	2.8	20	77	16	67	35	13	11	39	1.80
3957712--3957737	10	2.6	10	100	0	52	26	7	0	65	1.20
3960914--3960969	27	2.1	27	89	0	85	23	35	16	25	1.94
3969285--3969324	18	2.2	18	95	0	71	22	12	17	47	1.81
3972675--3972762	19	4.4	18	76	20	86	82	13	2	1	0.81
3972674--3972777	32	3.5	29	76	13	86	82	14	1	0	0.80
3972674--3972779	13	7.8	13	76	15	90	82	15	1	0	0.82
3972674--3972778	41	2.4	43	84	12	135	81	15	1	0	0.82
3972674--3972777	33	3.3	32	76	14	99	82	14	1	0	0.80
3974071--3974715	28	22.7	28	87	4	776	30	28	17	24	1.97
3974077--3974715	57	11.2	56	86	4	784	30	28	17	24	1.97
3974669--3974756	31	2.9	30	83	8	97	31	30	19	18	1.95
3976476--3976508	12	2.8	12	90	0	57	24	0	3	72	0.98
3977675--3977860	79	2.4	79	80	1	194	31	16	27	24	1.96
3977814--3977888	28	2.7	27	83	8	80	24	18	32	25	1.97
3977874--3978046	52	3.3	53	77	8	147	31	10	26	31	1.91
3977912--3978047	52	2.6	53	82	3	150	33	11	25	29	1.91
3978107--3978230	51	2.4	51	82	8	133	34	10	20	34	1.87
3980034--3980063	10	3.1	10	95	4	53	0	0	23	76	0.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3980576--3980642	33	2.0	33	88	0	98	43	16	14	25	1.86
3980597--3980622	13	2.0	13	100	0	52	38	15	15	30	1.88
3980662--3980716	19	2.9	19	97	0	101	40	14	10	34	1.81
3980779--3980818	21	1.9	21	100	0	80	40	17	10	32	1.83
3981577--3982093	55	9.3	55	82	11	520	23	21	27	27	1.99
3981599--3982098	102	4.5	103	81	9	405	24	21	27	26	1.99
3986621--3986693	20	3.6	20	81	3	101	35	13	19	31	1.91
3986621--3986715	41	2.3	42	96	1	174	40	12	17	29	1.87
3986754--3986779	13	2.0	13	100	0	52	38	15	15	30	1.88
3990842--3990880	15	2.6	15	91	0	60	51	15	20	12	1.76
3992888--3992965	20	3.6	21	73	15	70	25	12	16	44	1.83
3992952--3992990	13	3.0	13	96	0	69	30	17	15	35	1.91
3994796--3994841	16	2.8	16	93	6	74	28	2	39	30	1.69
3995448--3995520	20	3.6	20	81	3	101	35	13	19	31	1.91
3995448--3995542	41	2.3	42	96	1	174	40	12	17	29	1.87
3995581--3995606	13	2.0	13	100	0	52	38	15	15	30	1.88
3998804--3998837	17	2.0	17	88	0	50	5	26	17	50	1.69
4005488--4005564	28	2.8	28	82	4	75	25	19	31	23	1.98
4005549--4005722	51	3.4	51	81	8	192	32	11	25	31	1.91
4005582--4005768	51	3.7	49	80	10	180	33	11	25	29	1.91
4005752--4005826	27	2.7	27	89	6	107	22	20	33	24	1.97
4005437--4005933	263	1.9	264	85	3	698	31	13	25	29	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4007738--4007767	10	3.1	10	95	4	53	0	0	23	76	0.78
4008302--4008327	13	2.0	13	100	0	52	38	15	15	30	1.88
4008281--4008347	33	2.0	33	88	0	98	43	16	14	25	1.86
4008367--4008434	19	3.9	18	76	23	83	38	14	11	35	1.83
4008389--4008413	13	1.9	13	100	0	50	32	16	16	36	1.90
4008370--4008432	32	2.0	32	96	0	117	36	15	12	34	1.86
4008470--4008527	21	2.7	22	84	7	84	32	13	15	37	1.87
4009221--4009744	55	9.4	54	85	9	560	24	21	27	26	1.99
4009245--4009744	102	4.5	106	81	10	476	24	21	28	26	1.99
4009492--4009718	59	3.8	60	92	1	359	27	20	27	24	1.99
4015912--4015983	28	2.6	28	86	4	92	23	19	34	22	1.96
4015971--4016359	52	7.4	52	70	12	220	33	12	24	29	1.92
4016177--4016248	27	2.6	28	88	2	101	22	20	33	23	1.97
4016235--4016359	51	2.4	51	82	8	144	35	11	20	32	1.88
4015861--4016359	264	1.9	264	88	1	750	32	13	25	28	1.94
4018162--4018191	10	3.1	10	95	4	53	0	0	23	76	0.78
4018726--4018751	13	2.0	13	100	0	52	38	15	15	30	1.88
4018705--4018771	33	2.0	33	88	0	98	43	16	14	25	1.86
4018791--4018858	19	3.9	18	76	23	83	38	14	11	35	1.83
4018813--4018837	13	1.9	13	100	0	50	32	16	16	36	1.90
4018794--4018856	32	2.0	32	96	0	117	36	15	12	34	1.86
4018894--4018951	21	2.7	22	84	7	84	32	13	15	37	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4020373--4020612	98	2.5	97	77	5	243	27	27	13	31	1.94
4034275--4034470	91	2.2	91	98	0	374	38	18	14	28	1.90
4034457--4034527	20	3.6	20	79	7	83	33	14	12	39	1.83
4034577--4034630	20	2.7	20	88	2	72	33	14	14	37	1.88
4036200--4036238	15	2.6	15	84	11	53	43	0	28	28	1.55
4036752--4036802	21	2.4	21	83	6	59	58	13	5	21	1.56
4042022--4042077	19	2.9	19	83	2	67	35	12	17	33	1.88
4049076--4049110	15	2.3	15	90	0	52	25	31	0	42	1.55
4057099--4057307	50	4.2	50	73	6	190	35	22	19	22	1.96
4060100--4060374	148	1.9	149	81	6	344	36	12	11	39	1.79
4062238--4062263	13	2.0	13	100	0	52	38	15	15	30	1.88
4064478--4064522	21	2.1	21	84	8	56	53	4	20	22	1.63
4068371--4068450	20	3.8	20	75	15	79	26	15	15	43	1.85
4068436--4068474	13	3.0	13	96	0	69	30	17	15	35	1.91
4071010--4071035	13	2.0	13	100	0	52	38	15	15	30	1.88
4072391--4072485	45	2.1	44	80	3	109	36	16	18	27	1.93
4072107--4072581	50	9.6	50	70	8	175	33	17	20	27	1.96
4072567--4072680	48	2.3	50	83	4	151	36	13	21	28	1.91
4076845--4076965	52	2.3	52	97	0	224	28	18	18	34	1.94
4076845--4076985	52	2.7	51	90	4	212	30	17	18	33	1.94
4076974--4076998	13	1.9	13	100	0	50	36	16	16	32	1.90
4077064--4077088	13	1.9	13	100	0	50	32	16	16	36	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4077042--4077108	33	2.0	33	88	0	98	40	13	11	34	1.81
4082825--4082973	78	1.9	78	84	5	203	32	12	10	45	1.74
4084061--4084159	43	2.3	43	94	0	171	32	17	18	32	1.94
4085213--4085264	20	2.6	20	84	0	68	36	19	13	30	1.90
4085293--4085348	19	2.9	19	91	2	85	35	17	16	30	1.92
4085333--4085359	13	2.1	13	100	0	54	40	14	14	29	1.86
4085903--4085979	22	3.5	22	87	3	111	25	35	2	36	1.70
4092569--4092593	13	1.9	13	100	0	50	32	20	16	32	1.94
4095112--4095142	10	3.1	10	90	0	53	41	6	29	22	1.78
4095329--4095369	21	2.0	21	85	9	57	39	9	12	39	1.76
4100177--4100211	13	2.7	13	90	0	52	34	11	17	37	1.85
4102098--4102183	28	3.1	27	68	12	75	47	2	23	26	1.63
4102040--4102183	56	2.5	56	88	5	200	47	2	22	27	1.62
4102148--4102235	45	2.0	45	93	4	151	50	3	21	25	1.64
4102902--4102958	13	3.9	13	76	24	60	29	19	15	35	1.93
4102915--4102977	19	3.6	19	76	24	84	28	17	15	38	1.91
4102883--4102978	32	3.0	32	95	4	167	28	18	15	37	1.92
4106161--4106219	20	2.8	20	84	5	73	35	13	13	37	1.84
4106241--4106296	20	2.8	20	83	2	67	28	16	10	44	1.80
4108247--4108300	19	2.8	20	88	2	74	37	14	16	31	1.89
4108879--4109022	30	4.8	30	80	7	175	34	20	6	38	1.78
4108873--4109030	62	2.6	61	85	8	207	34	19	6	39	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4111028--4111074	23	2.0	23	91	0	76	42	14	10	31	1.80
4117081--4117105	13	1.9	13	100	0	50	32	16	16	36	1.90
4117061--4117125	33	2.0	32	85	11	87	33	18	13	33	1.90
4117814--4117876	32	1.9	33	87	9	94	30	19	14	36	1.91
4122256--4122346	41	2.3	41	79	9	100	36	2	31	29	1.70
4125401--4125473	20	3.6	20	81	3	101	35	13	19	31	1.91
4125419--4125494	21	3.7	21	78	3	91	40	11	17	30	1.85
4125401--4125494	41	2.3	41	96	0	170	38	12	18	30	1.88
4125533--4125558	13	2.0	13	100	0	52	38	15	15	30	1.88
4129621--4129651	15	2.1	15	93	0	53	48	16	22	12	1.80

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   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52