genome.fa.s2.2.7.7.80.10.50.1000.36.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: Scaffold2
Parameters: 2 7 7 80 10 50 1000
Length:  5794061

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   

This is table  36  of  38  ( 4457 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)
5508290--5508351	22	2.8	22	78	7	63	41	1	1	54	1.19
5509221--5509310	7	13.0	7	76	15	55	41	1	3	54	1.24
5512895--5513263	123	3.0	121	88	7	476	32	8	4	54	1.51
5513037--5513239	69	3.2	69	68	22	213	33	9	4	52	1.54
5512986--5513263	123	2.3	123	96	0	520	33	8	4	53	1.50
5513255--5513301	18	2.6	18	89	0	67	34	8	2	55	1.42
5518954--5519010	22	2.6	21	84	13	71	38	0	0	61	0.96
5520011--5520055	20	2.2	20	88	0	63	46	11	0	42	1.39
5520314--5520380	22	2.9	22	82	10	64	56	1	1	40	1.17
5523889--5523939	27	2.0	27	88	7	79	49	0	0	50	1.00
5524254--5524283	2	15.0	2	100	0	60	50	0	0	50	1.00
5524283--5524309	2	13.5	2	100	0	54	51	0	48	0	1.00
5524796--5524821	6	4.3	6	100	0	52	0	30	15	53	1.42
5528123--5528166	19	2.4	19	81	7	56	38	4	2	54	1.33
5528180--5528234	17	3.4	17	70	25	55	43	3	0	52	1.18
5528827--5528872	2	23.5	2	95	4	85	50	0	0	50	1.00
5536769--5536797	1	29.0	1	100	0	58	100	0	0	0	0.00
5539491--5539542	24	2.1	25	85	3	70	46	5	1	46	1.38
5539826--5539884	25	2.4	24	83	10	75	47	1	1	49	1.21
5544355--5544385	15	2.1	15	93	0	53	32	35	6	25	1.82
5550458--5550505	2	24.0	2	86	0	69	43	0	2	54	1.12
5553868--5554607	368	2.0	368	99	0	1471	38	17	17	26	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5556538--5556731	97	2.0	98	92	3	329	44	9	25	20	1.81
5557689--5557728	19	2.2	19	86	13	57	35	0	2	62	1.09
5557853--5557898	22	2.1	22	92	4	76	41	0	8	50	1.33
5558502--5558535	2	17.0	2	100	0	68	50	0	0	50	1.00
5559017--5559064	15	2.9	17	78	15	55	45	2	0	52	1.12
5559386--5559445	30	2.0	31	84	12	81	63	1	1	33	1.14
5559845--5559874	15	1.9	16	93	6	53	13	0	10	76	1.01
5560143--5560181	20	2.0	21	90	10	64	41	7	5	46	1.55
5561243--5561280	18	2.1	18	90	0	58	39	0	0	60	0.97
5561289--5561329	20	2.0	20	85	0	55	53	0	2	43	1.13
5566819--5566903	21	4.5	19	68	26	56	63	0	0	36	0.95
5566797--5566896	38	2.5	39	80	14	105	66	0	1	33	0.99
5566844--5566902	23	2.5	23	75	10	66	66	0	0	33	0.92
5566835--5566917	19	4.3	19	71	17	55	65	0	0	34	0.93
5566812--5566907	38	2.3	41	82	15	117	65	0	0	34	0.93
5569843--5569869	2	13.5	2	100	0	54	51	0	0	48	1.00
5571637--5571793	78	2.0	78	100	0	314	24	21	17	36	1.95
5573600--5573634	3	11.7	3	100	0	70	34	0	34	31	1.58
5581984--5582132	52	2.9	51	89	4	235	30	17	18	32	1.94
5582121--5582145	13	1.9	13	100	0	50	36	16	16	32	1.90
5582207--5582231	13	1.9	13	100	0	50	32	16	16	36	1.90
5582186--5582251	32	2.0	33	88	2	98	39	15	12	33	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5583063--5583274	52	4.2	51	75	12	179	33	16	25	25	1.96
5583174--5583259	43	2.0	43	90	0	136	27	18	25	27	1.98
5583263--5583704	30	15.1	30	77	10	326	25	16	28	28	1.97
5583294--5583709	58	7.1	57	75	12	292	24	16	29	29	1.97
5583526--5583700	29	6.0	29	81	6	183	26	17	28	26	1.98
5585135--5585246	1	112.0	1	80	0	116	0	0	9	89	0.54
5585135--5585243	11	9.7	11	86	10	134	0	0	10	88	0.55
5585135--5585246	29	3.8	29	85	9	147	0	0	9	89	0.54
5585135--5585247	50	2.3	48	89	4	172	0	0	10	88	0.56
5599122--5599270	52	2.9	51	89	4	235	30	17	18	32	1.94
5599259--5599283	13	1.9	13	100	0	50	36	16	16	32	1.90
5599345--5599369	13	1.9	13	100	0	50	32	16	16	36	1.90
5599324--5599389	32	2.0	33	88	2	98	39	15	12	33	1.84
5601249--5601283	15	2.4	15	95	4	63	17	20	5	57	1.60
5601311--5601485	5	35.0	5	87	0	179	22	20	9	48	1.77
5601311--5601484	15	11.6	15	89	0	231	22	20	8	48	1.76
5601308--5601485	20	8.6	20	83	6	230	21	19	8	49	1.76
5602379--5602409	16	2.0	15	93	6	53	77	3	0	19	0.90
5605991--5606029	20	2.0	20	89	0	60	56	0	0	43	0.99
5606146--5606189	10	4.4	10	82	8	54	31	2	2	63	1.19
5606156--5606197	21	2.1	19	91	8	66	33	4	0	61	1.17
5606165--5606197	11	3.1	11	86	4	50	30	6	0	63	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5606165--5606222	20	2.8	20	82	7	64	31	5	0	63	1.16
5606201--5606230	16	1.9	16	93	6	53	23	0	0	76	0.78
5606653--5606713	26	2.4	25	78	13	61	50	4	0	44	1.23
5606754--5606810	14	3.8	14	74	17	51	45	1	0	52	1.11
5606969--5607016	25	1.9	25	87	8	71	56	0	0	43	0.99
5607195--5607238	22	2.0	22	82	8	54	47	0	4	47	1.22
5607256--5607302	17	2.9	16	84	9	60	57	0	0	42	0.98
5608889--5608916	2	14.0	2	100	0	56	50	0	50	0	1.00
5613017--5613045	3	9.7	3	100	0	58	68	0	0	31	0.89
5613877--5613910	18	1.9	17	88	5	50	38	0	0	61	0.96
5614364--5614411	26	1.9	26	87	8	73	47	4	2	45	1.33
5614720--5614812	20	4.6	20	83	2	123	32	6	2	59	1.35
5614720--5614808	41	2.2	40	92	6	144	31	6	2	59	1.36
5614803--5614856	13	4.3	13	81	9	76	48	0	1	50	1.11
5614803--5614859	24	2.4	24	90	0	87	47	0	1	50	1.11
5619171--5619200	15	1.9	16	93	6	53	80	16	0	3	0.85
5621115--5621169	22	2.6	21	82	8	58	38	0	0	61	0.96
5621115--5621173	29	2.0	31	87	9	88	38	0	0	61	0.96
5621118--5621222	20	5.8	20	66	26	58	43	0	0	55	1.06
5621122--5621210	28	3.1	27	73	15	72	43	0	0	56	0.99
5621100--5621174	36	2.0	36	82	12	89	36	0	0	64	0.94
5621174--5621207	17	2.0	17	88	0	50	52	0	0	47	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5621144--5621248	51	2.0	52	82	14	128	48	0	0	50	1.07
5621667--5621697	1	31.0	1	93	0	53	0	3	0	96	0.21
5622954--5623049	50	1.9	50	93	0	165	43	20	15	19	1.87
5626307--5626331	2	12.5	2	100	0	50	52	0	0	48	1.00
5627105--5627151	2	23.5	2	91	0	76	48	4	0	46	1.21
5631130--5631186	23	2.4	24	80	11	64	66	1	0	31	1.02
5631200--5631259	31	1.9	32	90	10	97	43	1	0	55	1.10
5631235--5631286	19	2.7	19	91	5	79	42	3	0	53	1.19
5631317--5631354	14	2.8	14	84	4	51	47	2	0	50	1.15
5633487--5633563	39	2.0	39	89	0	118	35	15	11	37	1.84
5633634--5633663	15	2.0	15	93	0	51	76	3	13	6	1.11
5641868--5641924	13	3.9	13	76	24	60	35	14	17	33	1.90
5641846--5641943	19	5.8	18	70	28	81	33	13	16	36	1.87
5641852--5641945	32	2.9	32	95	1	161	36	12	15	35	1.86
5641986--5642010	13	1.9	13	100	0	50	32	16	16	36	1.90
5649211--5649264	17	3.3	16	73	14	56	83	5	9	1	0.88
5649211--5649262	26	1.9	26	88	7	77	82	5	9	1	0.90
5650210--5650365	31	5.1	31	81	10	169	22	29	15	32	1.95
5650339--5650497	34	4.8	34	76	17	156	22	32	11	33	1.89
5650329--5650524	62	3.0	63	83	7	191	20	31	11	36	1.88
5650428--5650497	35	2.0	34	83	5	86	20	32	10	37	1.85
5650464--5650542	27	2.9	27	88	0	122	22	30	13	32	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5650560--5650851	33	8.9	33	87	6	443	28	33	18	18	1.95
5650560--5650851	65	4.5	66	89	5	443	28	33	18	18	1.95
5650552--5650851	163	1.8	163	91	2	496	28	34	18	19	1.95
5650897--5651173	43	6.1	43	79	12	293	24	24	18	32	1.97
5650846--5651226	95	4.1	92	89	3	573	25	24	17	32	1.96
5650846--5651226	187	2.0	188	91	2	622	25	24	17	32	1.96
5651228--5651356	67	1.9	67	84	3	170	23	24	12	40	1.89
5652134--5652231	19	5.8	18	70	28	81	34	12	17	35	1.87
5652156--5652212	13	3.9	13	74	24	51	36	12	17	33	1.87
5652139--5652233	32	2.9	32	95	1	163	36	11	16	34	1.85

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