genome.fa.s10.2.7.7.80.10.50.1000.16.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: Chr10 ID=Chr10-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62175169

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   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190   191   192   
          193   194   195   196   197   198   199   200   201   202   

This is table  16  of  202  ( 24201 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)
4907284--4907447	49	3.5	46	72	15	129	28	21	16	32	1.95
4907947--4908010	30	2.1	31	88	2	94	28	25	6	40	1.79
4907957--4908004	15	3.2	15	74	11	53	29	20	8	41	1.81
4912697--4912721	13	1.9	13	100	0	50	12	8	0	80	0.92
4925786--4926041	44	5.8	43	74	7	176	26	16	27	30	1.96
4925775--4926041	131	2.0	132	92	0	446	26	15	27	29	1.96
4926048--4926801	82	9.2	82	94	0	1294	32	26	19	21	1.97
4931090--4931213	30	4.1	30	93	1	194	25	23	6	44	1.77
4931100--4931207	15	7.2	15	65	12	69	25	21	7	45	1.78
4933320--4933432	51	2.2	51	77	1	120	31	22	20	25	1.98
4933620--4934031	201	2.0	201	88	3	614	25	17	12	43	1.85
4934110--4934215	46	2.3	47	90	3	162	31	17	17	33	1.94
4934136--4934249	47	2.4	47	80	2	113	39	24	14	21	1.91
4934155--4938288	593	7.0	587	83	5	5037	31	17	15	36	1.91
4938663--4938778	51	2.2	52	81	6	137	31	21	18	29	1.97
4938655--4939811	626	1.8	627	86	3	1675	31	17	14	36	1.90
4940400--4940511	49	2.3	48	84	4	136	21	27	17	33	1.96
4939266--4943464	593	7.1	593	89	3	6105	30	18	14	36	1.90
4941608--4941706	49	2.0	49	86	5	139	24	21	17	37	1.94
4942184--4942354	46	3.6	46	72	11	128	24	23	16	35	1.95
4944319--4944431	47	2.4	47	80	5	120	24	23	16	34	1.95
4943470--4944754	591	2.2	590	90	2	2008	30	17	14	36	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4946324--4946452	30	4.4	29	75	7	100	35	21	3	38	1.72
4947003--4947056	14	3.6	15	78	12	58	61	1	37	0	1.07
4948254--4948405	48	3.1	48	78	2	115	25	23	17	34	1.96
4950034--4950151	49	2.4	49	80	5	130	28	27	13	30	1.94
4950618--4950642	3	8.3	3	100	0	50	68	0	0	32	0.90
4950707--4950807	49	2.1	48	83	1	121	29	20	16	32	1.95
4951834--4951997	51	3.3	51	71	7	147	26	20	15	37	1.92
4947933--4954865	595	11.7	591	87	3	9320	31	17	14	36	1.91
4953602--4953784	48	3.7	47	73	10	145	24	24	17	33	1.96
4955745--4955852	47	2.3	48	82	4	121	24	23	17	35	1.95
4954980--4956177	589	2.0	585	86	3	1661	31	17	14	36	1.90
4969757--4969795	18	2.2	17	86	13	53	33	0	20	46	1.51
4969900--4969928	8	3.6	8	100	0	58	24	13	27	34	1.93
4970015--4970089	23	3.3	23	94	1	134	21	20	26	32	1.97
4971260--4972579	415	3.2	415	92	1	2150	29	23	17	30	1.97
4978459--4978829	105	3.6	103	92	2	591	30	29	20	20	1.97
4981412--4981545	19	6.8	19	65	17	67	33	1	0	64	1.02
4981389--4981536	40	3.7	40	83	8	165	33	2	0	63	1.09
4981412--4981551	29	5.0	29	74	15	123	35	1	0	62	1.04
4981459--4981551	10	9.1	10	73	15	57	39	2	0	58	1.10
4981379--4981551	71	2.5	69	87	4	231	36	2	0	61	1.09
4981494--4981551	30	2.0	29	90	10	91	39	1	0	58	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4983183--4983240	28	2.1	27	84	9	73	43	3	3	50	1.36
4983425--4983456	14	2.2	15	94	5	57	50	12	9	28	1.71
4987281--4987322	18	2.5	17	81	18	52	42	40	0	16	1.48
4988718--4988778	10	6.6	9	88	7	63	49	4	0	45	1.23
4988718--4988779	6	10.3	6	92	0	97	48	4	0	46	1.23
4988718--4988779	8	7.8	8	92	0	97	48	4	0	46	1.23
4989353--4989403	13	3.9	13	75	14	52	37	1	1	58	1.20
4993476--4993501	13	2.0	13	100	0	52	23	23	23	30	1.99
4997741--4997775	18	2.0	17	88	5	52	20	25	0	54	1.45
4998298--4998323	5	5.2	5	100	0	52	42	19	19	19	1.90
4999066--4999125	30	2.0	30	83	3	75	41	0	38	20	1.52
4999339--4999375	9	4.1	9	89	0	56	29	8	13	48	1.71
5000745--5000777	4	8.2	4	100	0	66	24	0	24	51	1.48
5002099--5002130	16	2.0	16	100	0	64	43	31	0	25	1.55
5013875--5013910	16	2.1	18	90	10	58	22	0	5	72	1.05
5021396--5021436	16	2.6	16	81	18	50	26	2	7	63	1.33
5023834--5023871	11	3.6	10	89	10	58	44	0	0	55	0.99
5023836--5023872	10	3.4	11	92	7	58	43	0	0	56	0.99
5023854--5023908	25	2.2	25	90	3	83	30	0	3	65	1.10
5031691--5031742	26	2.0	26	92	0	86	61	3	3	30	1.32
5032774--5033007	46	5.6	43	82	13	235	35	14	21	28	1.93
5032812--5032922	37	3.0	37	93	0	186	38	13	19	27	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5035715--5035779	3	21.3	3	76	14	62	30	3	4	61	1.31
5035715--5035779	14	4.8	13	85	10	69	30	3	4	61	1.31
5035736--5035768	7	4.9	7	88	3	50	30	6	0	63	1.18
5040382--5040446	32	2.0	32	96	0	121	43	21	4	30	1.73
5042385--5042413	2	14.5	2	100	0	58	48	0	0	51	1.00
5048542--5048670	43	3.0	43	89	1	195	17	14	7	59	1.58
5048544--5048674	44	3.0	44	89	1	201	17	14	7	60	1.57
5049852--5049900	18	2.7	18	81	6	64	73	4	4	18	1.15
5073346--5073370	6	4.2	6	100	0	50	64	0	20	16	1.30
5074682--5074759	42	1.9	40	82	7	95	21	30	28	19	1.97
5078582--5078964	191	2.0	191	98	0	748	29	24	22	23	1.99
5080001--5080066	23	2.8	23	76	4	60	33	22	25	18	1.97
5079984--5080118	25	5.4	26	75	12	104	36	22	23	17	1.95
5080059--5080133	26	2.9	27	80	11	86	37	24	21	17	1.94
5082435--5082462	14	2.0	14	100	0	56	35	0	21	42	1.53
5082437--5082470	14	2.4	14	90	0	50	41	2	17	38	1.65
5085135--5085182	12	4.2	12	78	10	64	29	33	0	37	1.58
5085147--5085188	22	1.9	22	100	0	84	28	33	0	38	1.58
5086342--5086366	7	3.6	7	100	0	50	28	0	12	60	1.32
5087017--5087051	18	1.9	18	88	0	52	25	34	8	31	1.86
5087455--5087565	25	4.6	25	67	17	81	38	2	12	45	1.56
5087448--5087509	25	2.3	27	78	16	74	40	3	11	45	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5087453--5087633	71	2.5	71	90	2	292	37	2	13	46	1.57
5087513--5087636	36	3.5	35	64	11	90	37	1	12	47	1.52
5087636--5087688	23	2.7	18	75	25	61	52	18	0	28	1.46
5087645--5087689	23	2.0	23	100	0	90	51	17	0	31	1.46
5087658--5087819	29	5.6	29	92	4	272	43	27	1	27	1.63
5087658--5087819	59	2.8	58	91	4	272	43	27	1	27	1.63
5087658--5087819	88	1.9	87	92	3	272	43	27	1	27	1.63
5087868--5087892	10	2.5	10	100	0	50	44	8	0	48	1.32
5091002--5091351	123	2.8	124	93	0	603	32	21	16	29	1.95
5091933--5092003	35	2.1	35	87	10	103	71	11	1	15	1.20
5097340--5097383	18	2.4	18	76	3	52	70	4	0	25	1.06
5099060--5099130	2	36.0	2	80	8	74	49	2	4	43	1.36
5099201--5099234	2	17.5	2	93	6	61	50	0	0	50	1.00
5099919--5100017	41	2.4	41	82	0	135	23	20	29	27	1.99
5103934--5104113	89	2.0	88	93	2	288	31	12	12	43	1.79
5105971--5106001	7	4.3	7	95	4	53	25	0	0	74	0.82
5112170--5112224	28	2.0	28	92	0	92	27	25	14	32	1.95
5122685--5122743	28	2.1	28	87	0	82	32	20	16	30	1.95
5124456--5124504	18	2.8	18	81	3	55	61	0	2	36	1.08
5125742--5125841	51	2.0	51	84	4	130	48	1	26	25	1.58
5125800--5125853	11	4.8	12	84	15	71	44	0	31	24	1.54
5126109--5126168	30	2.0	30	96	0	111	36	21	8	33	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5129762--5129817	28	2.0	28	100	0	112	14	25	17	42	1.87
5134340--5134383	23	1.9	23	86	9	63	31	0	0	68	0.90
5134339--5134384	14	3.2	14	82	17	67	30	0	0	69	0.89
5134754--5134800	14	3.5	13	82	8	58	61	0	4	34	1.15
5136492--5136558	21	3.4	20	72	16	68	68	4	4	22	1.26
5137700--5137748	24	2.0	24	92	0	80	30	8	24	36	1.85
5143948--5144035	43	2.0	43	93	0	149	51	14	14	19	1.77
5145269--5145301	15	2.2	15	94	0	57	42	12	3	42	1.57
5146069--5146131	30	2.1	30	87	0	90	25	3	14	57	1.52
5148915--5149099	46	4.0	46	91	1	300	35	9	26	28	1.87

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   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190   191   192   
          193   194   195   196   197   198   199   200   201   202