genome.fa.s64.2.7.7.80.10.50.1000.29.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: Scaffold64
Parameters: 2 7 7 80 10 50 1000
Length:  7997333

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   

This is table  29  of  45  ( 5312 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)
5130912--5130960	20	2.4	20	82	3	53	36	24	12	26	1.91
5130879--5131089	112	1.9	113	85	3	291	33	23	13	29	1.93
5131745--5131900	71	2.2	72	85	2	215	44	13	18	23	1.85
5132095--5132309	73	3.0	71	78	8	195	37	13	22	26	1.92
5132091--5132343	70	3.5	71	78	8	244	37	13	22	25	1.91
5132756--5132912	72	2.2	72	82	3	181	45	14	21	18	1.85
5149827--5150081	61	4.2	61	86	2	359	24	27	19	28	1.99
5149821--5150095	123	2.2	123	86	2	383	24	26	19	29	1.98
5150011--5150200	99	1.9	99	88	4	285	25	28	16	29	1.97
5150103--5150380	60	4.5	60	82	5	326	25	28	19	27	1.98
5149881--5150760	222	3.9	222	73	12	637	24	28	18	28	1.98
5150108--5150374	123	2.2	122	88	4	394	25	27	19	26	1.99
5150572--5150829	61	4.3	60	85	9	332	25	26	21	26	1.99
5150594--5150832	122	2.0	122	89	5	367	24	26	20	28	1.99
5150813--5151003	42	4.5	42	80	9	199	20	25	15	38	1.92
5150808--5151007	87	2.3	85	86	5	260	20	25	15	40	1.90
5158371--5158438	28	2.4	28	90	4	102	25	33	16	25	1.95
5158535--5158645	51	2.2	52	85	6	147	35	23	7	34	1.82
5158584--5158801	79	2.7	77	76	11	215	29	22	13	34	1.92
5160665--5160702	2	19.5	2	83	5	51	47	2	0	50	1.15
5161373--5161398	2	13.0	2	100	0	52	50	0	0	50	1.00
5167067--5167102	17	2.2	16	90	5	54	25	0	0	75	0.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5167962--5168166	50	4.1	50	81	2	241	28	18	20	33	1.96
5167962--5168166	100	2.0	100	86	5	281	28	18	20	33	1.96
5169822--5169847	13	2.0	13	100	0	52	38	15	15	30	1.88
5169804--5169867	33	2.0	32	87	3	92	39	18	14	28	1.90
5175999--5176037	13	3.0	13	92	0	69	30	20	15	33	1.94
5178023--5178090	33	2.1	32	86	2	91	33	14	16	35	1.89
5180474--5180514	22	2.0	21	86	13	59	39	4	24	31	1.76
5180646--5180684	13	3.0	13	88	0	60	35	15	17	30	1.91
5186931--5186983	20	2.6	21	84	3	72	28	16	15	39	1.89
5186971--5186995	13	1.9	13	100	0	50	36	16	16	32	1.90
5188466--5188504	20	2.0	19	95	5	69	35	23	10	30	1.88
5188470--5188565	20	4.8	20	76	11	79	40	17	13	28	1.88
5188625--5188650	13	2.0	13	100	0	52	38	15	15	30	1.88
5188607--5188670	33	2.0	32	90	3	101	39	20	14	26	1.90
5192390--5192650	50	5.2	50	89	0	396	26	19	21	32	1.97
5193656--5193697	17	2.5	17	84	7	50	16	9	0	73	1.08
5193758--5193797	18	2.1	20	86	9	57	55	2	0	42	1.13
5193758--5193802	18	2.3	18	85	11	54	53	2	0	44	1.13
5193752--5193819	25	2.6	26	73	11	68	51	1	0	47	1.09
5196791--5196833	21	2.0	21	86	8	61	34	0	0	65	0.93
5196797--5196834	7	5.6	7	81	6	51	39	0	0	60	0.97
5202204--5202246	21	2.0	21	86	8	61	74	0	0	25	0.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5204143--5204366	112	2.0	112	88	0	333	35	18	21	24	1.95
5205373--5205408	17	2.0	19	89	10	58	38	5	11	44	1.63
5206547--5206592	2	23.0	2	100	0	92	50	0	0	50	1.00
5207370--5207403	14	2.4	14	90	0	50	61	8	0	29	1.26
5209895--5209932	16	2.4	16	82	8	51	44	21	15	18	1.86
5211342--5211415	28	2.7	28	89	2	114	28	21	29	20	1.98
5211265--5211494	106	2.2	107	81	3	259	32	15	26	25	1.96
5211371--5211545	79	2.2	77	88	6	260	30	16	28	25	1.96
5213846--5213885	20	2.0	20	100	0	80	40	10	15	35	1.80
5213903--5213928	13	2.0	13	100	0	52	38	15	15	30	1.88
5215779--5216139	79	4.6	78	90	3	535	31	15	26	26	1.96
5215781--5216139	157	2.3	157	90	3	580	31	15	26	26	1.96
5216094--5216170	28	2.8	28	86	7	104	24	22	29	23	1.99
5216094--5216166	27	2.7	26	87	6	92	24	21	30	23	1.99
5218604--5218645	21	2.0	21	95	0	75	33	21	4	40	1.74
5218662--5218734	32	2.3	32	90	0	110	36	17	10	34	1.85
5218689--5218713	13	1.9	13	100	0	50	32	16	16	36	1.90
5218701--5218762	19	3.2	19	69	13	54	27	17	14	40	1.89
5222998--5223062	8	8.0	9	74	23	56	55	0	1	43	1.09
5223008--5223076	14	5.4	14	75	23	55	55	0	1	43	1.08
5222997--5223056	22	2.7	22	80	17	70	56	0	1	41	1.09
5223016--5223080	8	8.6	8	75	21	61	52	0	1	46	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5222992--5223093	38	2.7	39	81	6	113	55	0	1	42	1.11
5223387--5223419	15	2.3	15	89	5	50	75	0	24	0	0.80
5225604--5225646	21	2.0	21	82	8	52	74	4	16	4	1.16
5226422--5226459	19	2.0	19	89	0	58	39	2	2	55	1.28
5226468--5226513	24	2.0	23	86	4	65	32	0	0	67	0.91
5226734--5226778	17	2.4	18	85	10	56	31	2	2	64	1.18
5226722--5226818	24	4.2	23	79	9	81	37	1	2	59	1.16
5226790--5226827	20	1.9	20	88	0	58	34	0	2	63	1.09
5230232--5230263	13	2.4	14	94	5	57	50	0	0	50	1.00
5230237--5230482	131	1.9	130	89	5	390	42	2	1	53	1.25
5230250--5230577	131	2.6	128	82	11	369	41	3	1	53	1.28
5232518--5232734	34	6.4	34	85	2	276	25	7	26	40	1.82
5232518--5232734	102	2.1	101	89	1	335	25	7	26	40	1.82
5233238--5233310	29	2.6	28	77	12	85	36	0	2	60	1.11
5234917--5234969	22	2.5	20	79	8	61	64	0	0	35	0.94
5235280--5235320	2	20.5	2	94	0	73	48	0	2	48	1.14
5235499--5235543	11	4.4	11	81	13	51	77	2	0	20	0.87
5237204--5237244	16	2.6	16	84	0	55	14	7	0	78	0.96
5237197--5237243	17	2.7	17	83	9	60	14	6	0	78	0.93
5238226--5238341	41	2.8	41	88	2	171	32	16	25	25	1.96
5242943--5243272	166	2.0	164	84	4	430	39	6	6	48	1.54
5243238--5243262	13	1.9	13	100	0	50	28	0	0	72	0.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5245694--5245738	21	2.2	20	84	4	54	46	2	8	42	1.47
5250666--5250706	21	2.0	21	85	0	55	43	7	12	36	1.70
5251186--5251227	20	2.0	21	90	4	68	83	0	14	2	0.75
5251861--5251911	21	2.4	21	76	0	57	35	13	19	31	1.91
5253178--5253273	30	3.2	30	67	11	81	27	17	16	38	1.91
5253175--5253264	29	3.1	30	65	10	78	25	16	18	38	1.92
5253086--5253368	118	2.4	117	79	10	299	27	17	17	37	1.92
5253103--5253367	59	4.5	57	76	14	227	26	17	17	38	1.92
5253335--5253509	60	2.9	60	76	2	174	26	10	13	48	1.76
5254991--5255022	13	2.5	13	89	0	55	0	0	9	90	0.45
5255710--5255740	13	2.4	13	88	0	53	0	0	9	90	0.46
5256428--5256458	13	2.4	13	88	0	53	0	0	9	90	0.46
5254914--5257660	718	3.8	719	99	0	5457	34	16	17	31	1.93
5257145--5257176	13	2.5	13	89	0	55	0	0	9	90	0.45
5258881--5258953	27	2.7	27	80	0	92	21	15	34	28	1.94
5259456--5259503	18	2.7	18	87	6	62	29	27	0	43	1.55
5265404--5265462	26	2.3	26	82	5	75	62	1	0	35	1.05
5269303--5269354	24	2.2	24	96	0	95	44	25	9	21	1.82
5271989--5272028	17	2.3	18	82	4	55	30	0	0	70	0.88
5273632--5273685	26	2.0	28	89	10	85	62	0	0	37	0.95
5273632--5273692	29	2.1	29	87	3	86	63	0	0	36	0.94
5273638--5273740	36	2.9	36	71	16	88	66	2	0	30	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5275607--5275653	14	3.5	13	78	16	51	29	2	2	65	1.15
5277337--5277383	22	2.1	23	88	4	69	68	4	0	27	1.08
5277343--5277383	11	3.7	11	84	12	57	68	2	0	29	1.03
5277670--5277732	2	31.5	2	84	12	85	44	0	4	50	1.23
5279170--5279207	18	2.1	18	90	5	58	42	0	0	57	0.98
5279177--5279221	22	2.0	23	83	12	58	37	0	2	60	1.09
5279200--5279252	26	2.0	26	85	0	70	43	0	1	54	1.11
5281554--5281625	31	2.3	31	95	0	126	44	12	5	37	1.66
5286863--5286916	17	3.2	17	77	20	51	59	0	0	40	0.98
5287123--5287168	21	2.4	19	82	13	58	63	4	2	30	1.26

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