genome.fa.s8.2.7.7.80.10.50.1000.29.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: Scaffold8
Parameters: 2 7 7 80 10 50 1000
Length:  6381039

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   

This is table  29  of  33  ( 3942 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)
5207709--5207776	21	3.5	21	74	22	51	35	0	0	64	0.94
5207698--5207784	30	2.8	30	83	13	88	37	0	0	62	0.96
5208011--5208046	17	2.1	18	89	5	56	55	0	0	44	0.99
5208891--5208945	25	2.2	25	77	6	58	69	1	1	27	1.09
5211432--5211498	34	1.9	36	81	6	84	55	1	0	43	1.09
5216064--5216109	19	2.4	19	88	3	74	50	0	0	50	1.00
5216064--5216110	20	2.4	21	86	13	73	48	0	0	51	1.00
5232509--5232547	4	9.2	4	91	2	51	0	25	0	74	0.82
5239851--5239904	19	2.8	19	75	13	56	61	3	1	33	1.25
5240924--5240950	2	13.5	2	100	0	54	51	0	0	48	1.00
5240950--5240985	2	18.0	2	100	0	72	50	0	50	0	1.00
5243185--5243217	17	1.9	17	88	11	50	75	3	3	18	1.06
5243185--5243218	18	1.9	17	88	5	50	76	2	2	17	1.04
5243411--5243455	23	2.0	23	90	0	72	40	0	0	60	0.97
5243422--5243466	13	3.8	12	83	16	58	40	0	0	60	0.97
5243443--5243483	13	3.2	13	89	0	55	53	0	0	46	1.00
5244801--5244985	34	5.5	34	88	0	273	40	26	7	25	1.81
5249051--5249113	19	3.3	19	90	0	90	34	19	17	28	1.94
5249418--5249600	34	5.4	34	88	0	269	40	26	7	25	1.81
5263422--5263460	2	19.5	2	100	0	78	48	0	0	51	1.00
5264694--5264728	2	17.5	2	87	0	52	48	2	0	48	1.16
5265095--5265167	20	3.6	21	75	17	73	34	1	0	64	1.02
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5265117--5265178	20	3.0	21	79	6	65	38	0	0	61	0.96
5265101--5265177	12	6.6	12	75	8	61	37	1	0	61	1.05
5265101--5265178	22	3.6	22	75	15	67	38	1	0	60	1.05
5270712--5270752	17	2.4	17	83	0	55	63	0	0	36	0.95
5275587--5275629	2	21.5	2	95	0	77	53	0	0	46	1.00
5277150--5277206	2	29.0	2	92	3	98	47	0	1	50	1.11
5278078--5278111	2	17.0	2	100	0	68	50	0	0	50	1.00
5286343--5286392	19	2.8	19	79	11	61	48	0	0	52	1.00
5286338--5286385	19	2.5	21	83	16	68	41	0	0	58	0.98
5286464--5286510	20	2.2	21	81	7	60	48	0	0	51	1.00
5286894--5286935	17	2.4	18	92	4	68	57	0	0	42	0.99
5291871--5291899	2	14.5	2	100	0	58	51	0	0	48	1.00
5291942--5291967	3	8.7	3	100	0	52	34	0	0	65	0.93
5298867--5298912	19	2.3	19	85	7	56	34	2	0	63	1.07
5299149--5299195	17	2.7	19	78	18	57	48	0	4	46	1.21
5307307--5307334	3	9.3	3	100	0	56	67	0	0	32	0.91
5308442--5308486	22	2.1	22	84	8	58	48	2	0	48	1.13
5310910--5310945	18	2.0	18	89	10	56	19	13	16	50	1.79
5311570--5311607	19	2.1	19	85	5	51	7	21	0	71	1.11
5313864--5313894	2	15.5	2	93	0	53	0	48	3	48	1.17
5317917--5317949	5	6.6	5	96	0	57	84	0	15	0	0.61
5320361--5320577	34	6.4	33	80	9	249	41	26	7	25	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5320361--5320577	102	2.1	101	87	1	326	41	26	7	25	1.81
5332326--5332358	3	11.0	3	93	0	57	63	0	3	33	1.10
5334738--5334785	2	25.0	2	91	8	82	50	0	0	50	1.00
5341402--5341431	13	2.3	13	94	0	51	0	10	0	90	0.47
5341938--5341998	32	1.9	31	83	9	79	40	3	1	54	1.27
5348200--5348225	3	8.7	3	100	0	52	69	0	30	0	0.89
5348267--5348292	2	13.0	2	100	0	52	50	0	50	0	1.00
5349076--5349115	15	2.7	15	85	11	55	40	0	5	55	1.22
5349078--5349140	30	2.1	31	82	14	78	39	0	3	57	1.15
5349131--5349192	20	3.1	20	72	11	56	62	0	0	37	0.95
5349646--5349695	13	3.6	14	78	19	52	36	0	2	62	1.07
5349645--5349708	29	2.1	32	83	11	82	42	0	1	56	1.09
5351712--5351746	10	3.5	10	88	0	52	51	0	0	48	1.00
5355029--5355105	3	25.7	3	100	0	154	67	0	0	32	0.91
5358309--5358342	2	17.0	2	100	0	68	50	0	0	50	1.00
5358852--5358884	4	8.2	4	93	0	57	24	3	0	72	0.98
5359192--5359222	2	15.5	2	100	0	62	51	0	0	48	1.00
5359925--5359990	27	2.4	27	85	7	80	30	3	15	51	1.58
5366662--5366707	24	1.9	25	86	8	69	47	6	0	45	1.28
5373018--5373045	2	14.0	2	100	0	56	50	0	0	50	1.00
5373579--5373728	74	2.0	74	88	8	225	32	22	18	26	1.97
5377438--5377592	78	2.0	78	97	0	292	29	16	20	34	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5381500--5381536	2	18.5	2	100	0	74	51	0	48	0	1.00
5383505--5383551	22	2.2	22	84	3	60	76	14	2	6	1.08
5383669--5383714	18	2.6	18	89	0	65	45	26	26	2	1.65
5383678--5383722	18	2.5	17	82	10	63	44	28	24	2	1.66
5384654--5384690	17	2.2	18	90	9	60	5	13	0	81	0.86
5395175--5395211	2	18.5	2	89	10	58	48	2	0	48	1.15
5406463--5406488	2	13.0	2	100	0	52	50	0	50	0	1.00
5406722--5406812	24	3.4	26	77	17	80	35	2	2	60	1.21
5406762--5406835	29	2.4	32	82	14	95	35	0	1	63	1.03
5406762--5406835	32	2.5	31	80	14	84	35	0	1	63	1.03
5406946--5406987	18	2.3	18	83	4	57	35	2	2	59	1.23
5407229--5407254	1	26.0	1	100	0	52	0	0	0	100	0.00
5411210--5411242	17	2.0	17	88	5	50	39	0	0	60	0.97
5411465--5411543	39	2.0	39	97	0	149	51	10	10	27	1.67
5412080--5412145	28	2.4	28	87	2	98	28	4	16	50	1.65
5412135--5412204	24	2.8	25	89	6	99	21	8	25	44	1.80
5416659--5416729	27	2.6	27	84	6	90	25	7	21	46	1.76
5416714--5416777	25	2.6	24	87	7	85	23	7	23	45	1.79
5416714--5416783	24	2.8	25	87	6	90	22	8	24	44	1.81
5419356--5419395	14	2.6	16	88	11	57	35	0	0	65	0.93
5419597--5419656	31	2.0	31	83	9	79	51	3	0	45	1.17
5421268--5421306	15	2.8	13	82	17	51	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)
5421255--5421330	39	2.0	37	82	5	89	40	0	1	57	1.07
5421279--5421339	24	2.5	24	81	5	68	37	0	0	62	0.96
5428620--5428657	18	2.1	18	85	9	51	55	0	0	44	0.99
5428734--5428771	20	1.9	20	88	0	58	28	7	7	55	1.57
5428807--5428905	43	2.3	43	85	0	135	41	6	3	49	1.43
5428800--5428900	22	4.7	22	75	10	84	39	5	3	50	1.45
5430508--5430550	21	2.0	21	86	0	59	44	0	0	55	0.99
5437745--5437793	2	24.5	2	91	0	62	51	8	0	40	1.32
5437745--5437793	14	3.5	14	85	0	71	51	8	0	40	1.32
5437955--5437997	15	2.8	16	79	10	54	55	0	0	44	0.99
5438322--5438366	2	23.0	2	81	4	56	53	2	0	44	1.13
5444941--5444997	3	18.7	3	92	3	96	29	0	0	70	0.88
5445217--5445276	18	3.3	18	88	0	84	40	0	6	53	1.27
5445217--5445292	18	4.3	18	81	5	75	39	1	6	52	1.36
5448023--5448097	18	4.2	18	87	0	114	44	1	1	53	1.17
5448084--5448114	16	1.9	16	93	0	53	35	0	9	54	1.33
5455454--5455481	4	7.0	4	100	0	56	25	25	0	50	1.50
5461665--5461700	5	7.2	5	90	0	54	58	5	0	36	1.22
5462757--5462876	25	4.5	27	70	20	92	61	0	0	37	1.02
5462757--5462844	29	2.9	28	83	14	97	62	0	0	37	0.95
5463173--5463198	13	2.0	13	100	0	52	84	0	0	15	0.62
5465301--5465341	22	1.9	21	85	5	55	56	0	2	41	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5465431--5465464	2	17.0	2	93	0	59	50	2	0	47	1.16
5467323--5467395	30	2.4	30	75	11	76	34	2	2	60	1.25
5467585--5467629	11	3.9	11	78	21	56	64	0	0	35	0.94
5467585--5467636	24	2.5	20	80	20	61	63	0	0	36	0.95
5467623--5467681	18	3.5	18	68	17	54	50	0	0	49	1.00
5467626--5467694	20	3.8	19	69	25	60	50	0	0	49	1.00
5467635--5467684	17	3.1	17	72	27	54	48	0	0	52	1.00
5467614--5467710	32	2.9	32	83	9	97	53	0	0	46	1.00
5467622--5467723	35	2.9	35	80	9	95	53	0	0	46	1.00
5470757--5470783	5	5.4	5	100	0	54	40	18	0	40	1.51

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