genome.fa.s25.2.7.7.80.10.50.1000.29.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: Scaffold25
Parameters: 2 7 7 80 10 50 1000
Length:  9553305

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   53   54   55   56   

This is table  29  of  56  ( 6609 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)
4938107--4938164	29	2.0	28	87	12	82	46	1	0	51	1.11
4939054--4939087	16	2.1	17	88	5	52	38	0	0	61	0.96
4939030--4939093	22	3.0	21	73	6	58	37	1	0	60	1.06
4939028--4939101	37	2.0	37	82	10	89	40	2	0	56	1.13
4939385--4939729	180	1.9	179	87	5	506	44	8	5	42	1.56
4943379--4943423	2	23.5	2	84	8	58	55	0	2	42	1.12
4944306--4944349	3	14.7	3	95	0	79	65	2	31	0	1.05
4945664--4945878	93	2.3	93	82	10	242	26	8	41	23	1.83
4945760--4946035	147	1.9	145	85	3	358	26	7	40	25	1.82
4946001--4946589	132	4.3	133	88	7	826	23	7	41	27	1.82
4946300--4946722	148	2.8	149	88	2	600	24	8	40	26	1.83
4946643--4946759	54	2.2	54	93	3	200	20	9	43	26	1.82
4947072--4947122	16	3.3	15	78	13	59	74	7	0	17	1.05
4947072--4947122	15	3.4	14	81	13	57	74	7	0	17	1.05
4947065--4947118	21	2.5	20	82	14	56	74	5	0	20	1.02
4947434--4947477	22	2.0	22	86	4	63	59	6	0	34	1.24
4948730--4948898	48	3.5	48	76	3	169	24	7	45	22	1.77
4948870--4948936	30	2.2	30	97	0	125	23	2	46	26	1.67
4948901--4949849	48	19.8	48	76	3	674	26	5	46	21	1.73
4948900--4949852	144	6.6	144	77	3	871	26	5	46	21	1.73
4949141--4949277	27	5.5	27	63	19	73	25	5	48	20	1.70
4949581--4949846	141	1.9	141	90	2	361	27	6	45	21	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4952059--4952087	2	14.5	2	100	0	58	48	0	0	51	1.00
4952962--4953376	48	8.6	48	75	4	345	25	4	48	21	1.70
4952992--4953377	144	2.7	145	84	2	499	25	5	47	21	1.71
4959547--4959721	48	3.7	47	75	3	152	27	5	43	24	1.75
4959547--4959721	96	1.8	96	88	0	269	27	5	43	24	1.75
4959637--4959785	81	1.8	81	91	0	244	26	4	45	23	1.72
4959683--4959749	33	2.0	33	91	0	107	29	5	41	22	1.77
4959716--4960306	48	12.4	48	75	2	519	26	3	46	23	1.68
4959469--4959915	177	2.6	175	86	5	599	28	4	42	24	1.74
4959895--4959929	15	2.3	15	90	0	52	22	0	60	17	1.37
4959765--4960207	234	1.9	234	90	0	715	25	3	46	23	1.67
4959730--4960408	96	7.1	96	81	5	496	26	3	46	23	1.69
4959769--4960295	234	2.2	233	86	2	631	26	3	46	23	1.68
4960006--4960414	96	4.1	102	85	6	536	26	3	46	22	1.67
4960374--4960420	6	7.8	6	76	9	51	19	0	61	19	1.34
4960411--4960498	30	3.2	30	64	26	86	32	4	45	17	1.68
4960138--4960463	102	3.2	102	86	5	331	28	3	46	21	1.66
4960389--4960526	51	2.6	55	85	12	205	28	2	50	18	1.62
4960404--4960520	51	2.3	51	100	0	234	30	3	47	17	1.64
4960411--4960493	27	3.2	27	63	16	75	33	4	44	16	1.69
4960510--4960541	3	10.7	3	93	0	55	3	0	68	28	1.04
4962129--4962153	2	12.5	2	100	0	50	48	0	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4966604--4966633	2	15.0	2	100	0	60	50	0	50	0	1.00
4969873--4969907	2	17.5	2	100	0	70	51	0	48	0	1.00
4971016--4971044	2	14.5	2	100	0	58	51	0	0	48	1.00
4972965--4972998	15	2.2	16	90	10	54	67	0	2	29	1.05
4973138--4973261	8	15.9	8	70	17	57	36	0	0	62	1.01
4973145--4973232	19	4.6	20	73	17	62	39	0	1	59	1.05
4973213--4973281	11	5.8	11	74	15	66	33	0	0	66	0.92
4973167--4973316	53	2.7	57	72	15	136	38	0	0	60	1.02
4973167--4973256	19	4.9	19	76	15	82	35	0	1	63	1.02
4973256--4973328	19	3.7	19	73	12	60	42	0	0	57	0.98
4973292--4973346	19	2.8	20	80	5	58	49	0	0	50	1.00
4973349--4973408	15	4.4	14	76	20	56	58	0	0	41	0.98
4973992--4974106	16	7.2	16	69	7	72	17	13	26	43	1.85
4973997--4974106	32	3.4	32	68	5	87	17	13	27	41	1.87
4973997--4974119	16	7.7	16	72	7	70	17	14	28	39	1.89
4975155--4975225	16	4.5	15	82	10	70	30	11	11	46	1.75
4975154--4975225	32	2.2	32	85	7	101	30	11	12	45	1.77
4975884--4975915	6	5.7	6	85	14	50	68	0	0	31	0.90
4975906--4975950	22	2.0	22	83	8	56	60	0	0	40	0.97
4975856--4975974	58	2.1	58	84	12	156	58	0	0	40	1.04
4975875--4975958	20	4.2	20	72	17	68	58	0	0	41	0.98
4976922--4976985	30	2.1	30	83	11	78	65	0	0	34	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4976924--4977012	25	3.7	24	72	21	62	61	1	0	37	1.03
4978352--4978386	15	2.3	15	85	0	52	14	22	0	62	1.31
4983490--4983528	18	2.2	18	85	0	51	12	17	0	69	1.19
4987592--4987627	18	2.0	18	88	0	54	11	30	0	58	1.33
4990561--4990604	21	2.1	21	87	8	63	43	0	0	56	0.99
4990599--4990640	21	2.1	19	86	13	57	57	0	0	42	0.99
4990769--4990918	70	2.1	70	90	6	241	48	2	12	36	1.56
4990906--4990959	18	3.0	18	80	0	63	50	3	7	38	1.48
4991337--4991395	31	1.9	32	86	6	86	47	5	1	45	1.34
4991503--4991543	20	2.0	21	85	4	57	19	12	0	68	1.21
5001032--5001062	10	3.1	10	95	0	53	51	12	0	35	1.40
5002531--5002561	15	2.1	15	93	0	53	29	0	6	64	1.18
5004491--5004527	18	2.0	19	89	5	58	67	0	0	32	0.91
5005216--5005253	15	2.4	16	83	16	53	52	2	0	44	1.14
5005512--5005552	20	2.0	20	86	9	57	46	2	0	51	1.14
5005684--5005735	2	26.0	2	100	0	104	50	0	0	50	1.00
5005940--5005982	2	21.5	2	95	0	77	48	2	48	0	1.14
5011221--5011251	15	2.1	15	94	5	55	64	0	6	29	1.18
5011702--5011758	16	3.6	16	76	9	53	35	3	10	50	1.54
5011699--5011774	32	2.4	31	74	8	73	31	2	9	56	1.45
5012131--5012169	18	2.2	18	85	0	51	61	5	0	33	1.18
5015335--5015374	22	1.9	20	85	10	53	55	2	2	40	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5016115--5016140	3	8.7	3	100	0	52	69	0	30	0	0.89
5017491--5017534	22	2.0	22	90	0	70	56	2	0	40	1.11
5018526--5018578	23	2.3	24	84	12	67	49	3	1	45	1.31
5019933--5019966	12	2.8	12	86	0	50	44	5	0	50	1.26
5019949--5019985	17	2.1	18	90	5	58	43	5	0	51	1.24
5020032--5020088	17	3.2	18	75	9	55	61	8	1	28	1.36
5020177--5020228	15	3.5	15	82	7	61	65	0	1	32	1.04
5020182--5020229	16	3.1	16	81	3	53	66	0	2	31	1.03
5028025--5028067	2	21.5	2	100	0	86	51	0	48	0	1.00
5028173--5028234	28	2.1	30	91	5	101	54	12	6	25	1.62
5029931--5029969	18	2.2	18	86	9	53	41	12	5	41	1.65
5030417--5030444	14	2.0	14	100	0	56	28	7	14	50	1.69
5031364--5031406	15	2.9	15	89	0	59	53	0	0	46	1.00
5031398--5031452	15	3.8	15	81	11	62	60	0	1	38	1.08
5031383--5031433	22	2.4	21	90	6	84	56	0	0	43	0.99
5033588--5033623	5	7.2	5	100	0	72	58	0	0	41	0.98
5034850--5034960	54	2.1	54	91	0	177	39	15	19	25	1.91
5037826--5037871	18	2.5	18	85	3	56	30	4	2	63	1.26
5040119--5040162	2	22.0	2	100	0	88	50	0	50	0	1.00
5043623--5043656	2	17.0	2	93	0	59	50	2	0	47	1.16
5048415--5048489	20	3.8	20	80	3	80	40	12	13	34	1.81
5048412--5048489	40	2.0	39	87	2	111	39	12	12	34	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5052082--5052137	19	2.8	19	78	5	58	53	0	1	44	1.11
5052981--5053039	29	2.1	27	84	12	75	69	1	3	25	1.13
5053693--5053730	17	2.3	17	81	4	51	39	2	0	57	1.12
5053894--5053928	17	2.1	17	88	0	52	37	0	2	60	1.12
5055745--5055847	50	2.1	49	81	1	116	51	0	2	45	1.16
5060404--5060448	19	2.4	19	92	3	74	46	0	0	53	1.00
5063429--5063488	14	4.4	14	70	16	54	66	0	0	33	0.92
5063428--5063488	28	2.2	28	86	11	83	65	0	0	34	0.93
5063430--5063481	13	4.0	12	74	16	50	67	0	0	32	0.91
5063664--5063703	21	1.9	21	94	0	71	0	25	15	60	1.35

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   53   54   55   56