genome.fa.s2.2.7.7.80.10.50.1000.33.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  33  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)
5035818--5035895	31	2.5	31	91	0	120	41	15	16	26	1.88
5036073--5036099	13	2.1	13	100	0	54	22	22	22	33	1.97
5036219--5036271	20	2.6	20	84	3	61	43	9	15	32	1.78
5036234--5036272	20	2.0	20	94	0	69	43	12	15	28	1.83
5037576--5037702	35	3.4	35	73	16	112	19	25	16	37	1.93
5037609--5037833	43	5.5	43	73	13	197	19	26	14	39	1.90
5037576--5037833	78	3.2	78	87	4	340	19	26	15	39	1.91
5038208--5038399	31	6.2	31	69	2	143	29	33	21	15	1.94
5038196--5038399	62	3.3	62	88	0	264	29	32	22	15	1.95
5042372--5042466	50	1.9	50	84	0	127	46	12	10	30	1.76
5043783--5043825	20	2.1	21	87	12	63	58	23	0	18	1.40
5047296--5047331	17	2.1	17	89	0	54	83	0	16	0	0.65
5047864--5047913	23	2.2	24	79	13	61	38	2	6	54	1.37
5053747--5053827	36	2.3	35	81	10	85	71	9	13	4	1.28
5055158--5055923	27	27.9	27	89	3	1111	23	33	13	29	1.93
5055158--5055923	55	14.0	54	91	2	1111	23	33	13	29	1.93
5055158--5055923	82	9.3	81	89	3	1111	23	33	13	29	1.93
5055909--5056448	32	16.8	32	92	1	841	31	32	19	16	1.94
5057688--5057723	17	2.1	17	89	0	54	83	0	16	0	0.65
5062009--5062221	57	3.7	58	75	10	204	48	13	7	30	1.71
5062107--5062186	29	2.8	28	70	21	67	51	15	2	31	1.56
5062223--5062313	47	1.9	47	84	8	123	52	9	12	25	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5064836--5064892	21	2.7	21	83	5	71	35	14	14	36	1.86
5065133--5065179	22	2.1	22	100	0	94	36	6	29	27	1.82
5067380--5067420	2	20.5	2	94	0	73	0	51	0	48	1.00
5071864--5071899	18	2.0	18	94	0	63	47	16	16	19	1.83
5074007--5074040	2	17.0	2	93	0	59	52	0	47	0	1.00
5074795--5074828	2	17.0	2	100	0	68	50	0	50	0	1.00
5076816--5076871	17	3.2	17	82	9	69	76	0	1	21	0.87
5076816--5076871	9	6.3	9	78	10	62	76	0	1	21	0.87
5080012--5080125	32	3.6	32	73	4	113	17	13	27	42	1.86
5080081--5080119	16	2.4	16	86	0	51	15	12	28	43	1.83
5082009--5082291	76	3.7	77	75	7	243	39	15	13	30	1.86
5089779--5089907	52	2.5	52	94	0	231	28	17	17	35	1.93
5089916--5089940	13	1.9	13	100	0	50	36	16	16	32	1.90
5092349--5092376	14	2.0	14	100	0	56	42	0	14	42	1.45
5094056--5094105	20	2.5	22	78	18	63	46	14	12	28	1.79
5093889--5094109	92	2.4	91	80	6	241	39	15	13	31	1.85
5098027--5098052	13	2.0	13	100	0	52	30	15	15	38	1.88
5098760--5098803	21	2.1	21	83	8	54	25	31	4	38	1.76
5100589--5100614	13	2.0	13	100	0	52	38	15	15	30	1.88
5102693--5102723	15	2.1	15	93	0	53	12	22	16	48	1.80
5104527--5104571	21	2.1	21	88	8	65	22	17	4	55	1.60
5106785--5106810	13	2.0	13	100	0	52	30	15	15	38	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5109981--5110071	42	2.2	42	91	0	146	39	18	14	27	1.89
5112479--5112504	13	2.0	13	100	0	52	38	15	15	30	1.88
5116890--5117010	52	2.3	52	97	0	224	28	18	18	34	1.94
5116890--5117030	52	2.7	51	90	4	212	30	17	18	33	1.94
5117019--5117043	13	1.9	13	100	0	50	36	16	16	32	1.90
5117109--5117133	13	1.9	13	100	0	50	32	16	16	36	1.90
5117087--5117153	33	2.0	33	88	0	98	40	13	11	34	1.81
5118321--5118365	21	2.1	22	88	8	67	55	4	17	22	1.60
5120168--5120198	15	2.1	15	93	0	53	48	16	22	12	1.80
5122283--5122308	13	2.0	13	100	0	52	30	15	15	38	1.88
5122429--5122474	21	2.2	20	81	11	58	32	19	4	43	1.71
5124864--5124889	13	2.0	13	100	0	52	38	15	15	30	1.88
5128426--5128460	16	2.2	16	94	0	61	34	0	2	62	1.10
5128433--5128467	16	2.1	16	89	5	52	34	2	2	60	1.26
5129552--5129588	3	12.3	3	100	0	74	32	0	0	67	0.91
5129725--5129756	16	1.9	17	93	6	57	56	9	0	34	1.32
5129992--5130033	22	1.9	22	90	9	68	61	0	0	38	0.96
5130325--5130396	30	2.4	29	84	8	92	54	1	0	44	1.08
5132987--5133046	20	2.8	21	80	12	61	55	0	0	45	0.99
5133977--5134017	22	1.9	22	85	14	59	56	7	2	34	1.40
5138140--5138183	21	2.1	21	86	0	61	4	15	34	45	1.67
5138152--5138193	12	3.5	12	78	12	50	2	21	35	40	1.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5141389--5141468	36	2.2	36	93	0	133	33	32	12	21	1.91
5145299--5145342	21	2.1	21	86	0	61	2	15	31	50	1.57
5145299--5145345	18	2.6	18	83	6	51	2	17	31	48	1.58
5146440--5146476	19	2.0	19	89	5	58	27	0	0	72	0.84
5146724--5146758	15	2.2	16	90	5	54	37	0	2	60	1.12
5146722--5146759	16	2.4	17	82	13	53	36	0	2	60	1.11
5151851--5151875	2	12.5	2	100	0	50	52	0	0	48	1.00
5167702--5167832	65	2.0	66	98	1	255	33	25	7	32	1.84
5169280--5169305	13	2.0	13	100	0	52	23	30	7	38	1.83
5169374--5169424	11	5.0	10	79	11	50	74	1	21	1	1.02
5174170--5174194	13	1.9	13	100	0	50	36	16	16	32	1.90
5174235--5174301	33	2.0	33	88	0	98	40	13	11	34	1.81
5174257--5174281	13	1.9	13	100	0	50	32	16	16	36	1.90
5174339--5174380	21	2.0	21	90	0	66	35	14	14	35	1.86
5177545--5177607	15	3.9	15	82	12	72	1	0	17	80	0.78
5177545--5177608	12	5.2	12	78	14	69	1	0	17	81	0.77
5184562--5185857	49	25.8	49	83	6	1427	32	18	26	22	1.97
5184620--5185857	101	12.3	99	84	6	1374	32	18	26	22	1.97
5184562--5185857	150	8.6	148	86	3	1591	32	18	26	22	1.97
5185885--5185998	35	3.2	36	87	6	171	40	10	28	20	1.85
5186010--5186172	62	2.6	64	80	7	174	32	14	31	22	1.93
5186000--5186172	31	5.5	31	79	12	140	31	13	31	23	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5187460--5187528	12	6.1	11	78	11	68	2	1	13	82	0.85
5187475--5187528	6	9.5	6	78	11	60	1	1	12	83	0.81
5187460--5187528	16	4.2	16	80	9	68	2	1	13	82	0.85
5187463--5187528	22	2.9	22	76	19	64	3	1	13	81	0.87
5187460--5187518	16	3.5	16	82	11	73	1	0	13	84	0.69
5187460--5187528	33	2.0	35	86	5	97	2	1	13	82	0.85
5187478--5187535	28	2.1	28	83	6	73	1	1	17	79	0.90
5192557--5192685	52	2.5	52	96	0	240	28	18	18	34	1.95
5194263--5194334	28	2.6	28	80	4	74	25	15	33	26	1.95
5194322--5194438	51	2.3	50	78	8	128	31	12	24	30	1.93
5194292--5194573	130	2.2	132	82	8	351	31	11	26	30	1.92
5194452--5194733	52	5.6	51	77	7	263	34	9	25	30	1.88
5194453--5194733	96	2.8	101	82	7	340	34	9	24	30	1.88
5197182--5197233	21	2.6	21	90	6	81	32	15	13	38	1.86
5200680--5200725	23	2.1	21	88	8	65	52	0	0	47	1.00
5200686--5200733	21	2.2	22	85	7	62	62	0	0	37	0.95
5201297--5201330	11	2.8	12	83	16	52	29	0	0	70	0.87
5201398--5201442	18	2.4	19	81	3	56	42	6	2	48	1.41
5201959--5201997	21	1.9	20	94	5	69	35	10	12	41	1.77
5202801--5203544	30	24.7	30	75	11	472	28	28	15	27	1.96
5202805--5203544	59	12.3	59	71	12	295	28	28	15	27	1.97
5202801--5203544	211	3.5	210	89	3	1032	28	28	15	27	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5203375--5203466	35	2.7	35	83	5	107	19	28	13	39	1.89
5203685--5203773	43	2.1	43	91	0	142	28	23	17	30	1.97
5203634--5203814	92	1.9	94	91	3	294	27	24	16	30	1.97
5203727--5203880	52	2.9	53	80	4	184	24	24	16	35	1.95
5204715--5204739	13	1.9	13	100	0	50	36	16	16	32	1.90
5204695--5204761	33	2.0	33	85	0	89	34	11	13	40	1.81
5204802--5204826	13	1.9	13	100	0	50	32	16	16	36	1.90
5204835--5205015	52	3.5	52	97	0	335	34	18	17	29	1.94
5217369--5217411	21	2.0	20	83	16	52	41	2	4	51	1.35
5218645--5218697	17	3.3	17	69	15	58	49	20	5	24	1.71

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