genome.fa.s11.2.7.7.80.10.50.1000.12.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: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62681010

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   203   204   205   206   207   208   
          209   210   

This is table  12  of  210  ( 25152 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)
4513687--4513822	42	3.2	42	80	0	155	44	20	19	16	1.87
4513714--4513782	21	3.3	20	78	9	68	43	18	20	17	1.88
4515976--4516005	15	2.0	15	100	0	60	26	20	26	26	1.99
4518807--4518838	2	16.0	2	100	0	64	50	0	0	50	1.00
4520295--4520322	3	9.3	3	100	0	56	32	0	0	67	0.91
4521392--4521435	22	2.0	22	81	4	52	38	4	2	54	1.33
4522528--4522565	18	2.2	18	85	4	51	13	23	2	60	1.45
4531748--4531773	2	13.0	2	100	0	52	50	0	0	50	1.00
4541016--4541254	119	2.0	119	99	0	469	28	15	18	36	1.92
4542175--4542204	15	2.1	15	93	6	53	23	20	3	53	1.60
4545010--4545082	24	3.0	24	81	0	92	23	28	16	31	1.96
4547438--4547473	2	18.0	2	88	0	54	50	0	2	47	1.15
4551471--4551514	24	1.9	23	86	9	63	61	2	6	29	1.34
4552778--4552810	12	2.9	12	86	13	52	75	9	6	9	1.18
4555429--4555488	21	2.9	21	79	0	66	15	28	16	40	1.89
4559307--4559342	18	2.1	18	94	5	65	41	16	19	22	1.90
4582672--4582706	2	17.5	2	93	0	61	45	0	2	51	1.16
4588168--4588297	45	2.9	44	85	3	170	39	10	23	26	1.86
4588305--4588441	27	5.1	27	72	0	112	37	20	25	16	1.93
4588419--4588577	27	5.9	27	82	0	156	42	13	19	25	1.87
4588307--4588460	54	2.9	54	80	0	182	38	20	24	17	1.93
4588373--4588572	81	2.5	81	78	0	211	42	14	20	23	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4588422--4588569	54	2.7	54	86	0	197	43	13	18	25	1.86
4588341--4588588	54	4.6	54	77	3	185	39	16	21	22	1.91
4590634--4590661	6	4.7	6	100	0	56	28	0	0	71	0.86
4596093--4596124	17	1.9	16	93	6	55	31	0	0	68	0.90
4597172--4597212	21	2.0	21	85	0	55	70	4	7	17	1.28
4605673--4605730	30	1.9	30	96	0	107	55	15	5	24	1.61
4611525--4611656	50	2.6	50	80	4	158	31	21	26	19	1.98
4613733--4613818	38	2.2	39	85	6	120	36	25	12	25	1.92
4613733--4613859	39	3.3	38	83	3	137	34	24	13	27	1.93
4613761--4613892	39	3.4	39	85	1	140	34	20	12	32	1.89
4615916--4615997	41	2.0	41	100	0	164	36	0	24	39	1.56
4623665--4623730	28	2.4	28	75	10	64	48	9	3	39	1.50
4625037--4625072	17	2.1	17	94	0	63	25	2	0	72	0.98
4630449--4630482	17	2.0	17	88	0	50	67	2	0	29	1.05
4631827--4631866	13	3.1	13	81	0	53	27	7	30	35	1.84
4642663--4642704	16	2.7	16	79	17	52	73	0	0	26	0.83
4642674--4642707	17	1.9	17	88	5	50	73	0	0	26	0.83
4661834--4661874	22	1.9	22	85	5	57	43	21	7	26	1.79
4666850--4666925	9	8.4	9	73	5	73	30	7	18	43	1.78
4666858--4666925	27	2.5	27	85	0	91	30	7	17	44	1.76
4668982--4669048	5	12.6	5	75	17	55	22	1	0	76	0.87
4668982--4669050	23	3.1	22	84	10	88	21	1	0	76	0.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4668988--4669062	21	3.4	21	82	12	89	22	4	0	73	1.00
4669158--4669232	12	6.4	11	72	13	51	12	6	4	77	1.10
4673880--4673945	10	6.7	10	78	13	57	54	3	4	37	1.36
4673930--4673973	16	2.7	16	89	3	61	63	0	0	36	0.95
4674521--4674570	20	2.5	20	87	9	66	38	4	2	56	1.30
4674521--4674579	21	2.8	21	85	12	68	38	3	1	55	1.26
4674539--4674618	30	2.7	29	83	9	99	37	1	2	58	1.19
4674521--4674587	21	3.3	20	83	6	64	40	2	1	55	1.24
4674535--4674617	10	8.6	9	69	18	51	36	1	2	60	1.18
4674595--4674665	30	2.4	29	86	11	92	26	8	2	61	1.38
4677131--4677209	37	2.2	37	84	11	101	49	0	8	41	1.34
4688775--4688821	14	3.4	14	77	11	51	23	0	6	70	1.10
4691283--4691416	23	6.0	23	89	2	184	38	23	20	17	1.93
4697522--4697669	45	3.2	46	79	5	172	52	18	4	24	1.63
4697531--4697671	48	3.0	47	83	3	196	50	19	4	25	1.67
4698919--4698957	13	2.9	14	81	11	55	25	17	0	56	1.41
4699062--4699196	37	3.4	40	72	13	118	31	25	17	25	1.97
4699370--4699413	2	22.0	2	100	0	88	50	0	0	50	1.00
4700160--4700201	2	21.5	2	86	13	61	50	0	2	47	1.14
4700185--4700253	34	2.0	34	81	10	79	44	7	2	44	1.46
4701369--4701397	6	4.8	6	100	0	58	86	0	13	0	0.58
4703146--4703190	18	2.4	19	92	3	74	37	13	0	48	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4704478--4704514	2	18.5	2	94	0	56	48	5	0	45	1.25
4708152--4708207	27	2.0	28	93	3	96	41	8	0	50	1.34
4708258--4708331	27	2.7	27	91	8	116	21	27	32	18	1.97
4708571--4708602	3	10.7	3	93	0	55	3	0	28	68	1.04
4711801--4711842	21	2.0	22	85	4	59	59	14	19	7	1.57
4717898--4717976	32	2.3	35	82	8	92	54	5	3	36	1.41
4718108--4718140	2	16.5	2	100	0	66	48	0	0	51	1.00
4718163--4718206	17	2.6	17	85	3	63	47	0	11	40	1.39
4718332--4718367	3	12.0	3	93	0	54	66	5	0	27	1.13
4720468--4720541	20	3.8	20	87	7	98	35	0	4	60	1.15
4720470--4720541	9	7.6	9	71	11	54	34	0	4	61	1.16
4730224--4730261	18	2.1	18	90	0	58	44	34	13	7	1.72
4730221--4730273	27	2.0	27	85	7	72	43	33	13	9	1.76
4730197--4730261	15	4.1	15	73	11	58	43	36	15	4	1.67
4734746--4734857	31	3.2	37	63	29	98	41	8	7	43	1.61
4734746--4734886	69	2.1	68	98	1	273	43	7	6	43	1.57
4738654--4738686	3	11.0	3	100	0	66	33	0	33	33	1.58
4743081--4743144	29	2.1	30	83	11	78	57	3	4	34	1.35
4749322--4749375	3	19.3	3	74	14	53	29	3	1	64	1.21
4749313--4749372	11	5.5	11	76	4	59	26	5	1	66	1.21
4750848--4750884	17	2.1	18	90	5	58	32	16	10	40	1.83
4753087--4753114	5	5.6	5	100	0	56	39	0	0	60	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4754064--4754100	18	2.1	18	100	0	74	45	16	32	5	1.70
4759251--4759275	13	1.9	13	100	0	50	64	0	0	36	0.94
4759444--4759473	9	3.3	9	95	0	51	46	0	0	53	1.00
4759445--4759481	17	2.1	18	90	5	58	51	0	0	48	1.00
4760678--4760743	19	3.5	19	79	4	89	50	1	10	37	1.47
4761060--4761128	27	2.6	27	92	0	111	17	31	23	27	1.97
4761176--4761250	28	2.7	28	89	2	107	41	0	9	49	1.35
4777289--4777350	30	2.1	30	84	6	81	30	33	11	24	1.90
4777488--4777518	3	10.3	3	100	0	62	0	32	0	67	0.91
4780759--4780805	24	1.9	25	83	12	62	57	2	4	36	1.30
4781808--4781861	12	4.5	12	85	0	72	0	11	22	66	1.22
4781808--4781861	24	2.2	24	93	0	90	0	11	22	66	1.22
4781808--4781861	6	9.0	6	76	8	56	0	11	22	66	1.22
4786384--4786453	27	2.6	27	80	8	79	25	2	21	50	1.63
4786422--4786489	35	2.0	33	83	13	86	29	2	17	50	1.61
4787895--4787934	14	2.9	14	84	0	53	42	17	7	32	1.77
4787860--4787926	34	1.9	35	87	3	100	44	13	10	31	1.77
4796164--4796199	18	2.0	18	100	0	72	38	5	0	55	1.23
4798966--4799057	37	2.5	37	91	7	134	32	5	15	46	1.68
4798988--4799048	17	3.4	17	70	12	59	31	3	14	50	1.59
4799056--4799086	9	3.4	9	95	0	53	25	9	22	41	1.84
4800101--4800153	13	4.1	13	80	0	52	33	0	20	45	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4800104--4800153	26	1.9	26	87	0	73	36	0	20	44	1.52
4813799--4813835	10	4.2	9	80	19	51	64	0	0	35	0.94
4813798--4813833	16	2.2	17	95	5	65	63	0	0	36	0.94
4820220--4820263	22	2.0	22	81	0	52	77	2	15	4	1.04
4820226--4820263	11	3.5	11	89	7	51	81	0	15	2	0.80
4820232--4820264	11	2.9	12	91	8	52	78	0	21	0	0.75
4822150--4822392	50	4.8	50	92	0	396	20	31	21	25	1.98
4822730--4822786	30	1.9	30	82	3	71	29	22	3	43	1.70
4823865--4823918	7	7.6	7	82	17	67	70	0	14	14	1.17
4823865--4823915	14	3.6	14	87	12	77	72	0	13	13	1.12

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   203   204   205   206   207   208   
          209   210