genome.fa.s8.2.7.7.80.10.50.1000.162.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   

This is table  162  of  190  ( 22705 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)
47268560--47268608	25	1.9	26	83	4	64	42	0	40	16	1.48
47268659--47268718	30	2.0	30	83	3	75	41	0	38	20	1.52
47269699--47269789	25	3.7	26	78	14	77	17	24	21	36	1.95
47269700--47269804	49	2.1	50	86	8	144	17	26	21	34	1.95
47270333--47270361	2	14.5	2	100	0	58	51	0	0	48	1.00
47271407--47271441	17	2.1	17	88	0	52	40	25	20	14	1.90
47274308--47274727	125	3.4	125	84	2	583	29	19	21	30	1.97
47277837--47277884	25	1.9	25	100	0	96	39	14	0	45	1.45
47277799--47277929	70	1.9	70	95	3	237	48	12	1	37	1.50
47278358--47278397	18	2.2	18	95	0	71	40	7	30	22	1.81
47280200--47280297	51	1.9	51	85	4	135	45	5	22	26	1.73
47280259--47280313	22	2.4	23	80	11	60	45	1	25	27	1.64
47283695--47283719	13	1.9	13	100	0	50	80	0	0	20	0.72
47287754--47287779	3	8.7	3	100	0	52	69	0	0	30	0.89
47304344--47304383	2	20.0	2	100	0	80	50	0	0	50	1.00
47304720--47304834	41	2.8	41	85	0	131	26	24	20	28	1.99
47304760--47304839	41	2.0	41	94	0	142	27	22	20	30	1.98
47305094--47305126	2	16.5	2	93	0	57	48	3	0	48	1.17
47306986--47307024	16	2.4	17	87	8	55	25	2	0	71	0.98
47314060--47314161	53	2.0	51	94	3	177	31	22	10	35	1.89
47315965--47316067	25	4.1	25	76	5	93	31	21	26	21	1.98
47315965--47316067	50	2.1	50	80	7	111	31	21	26	21	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47316026--47316079	25	2.2	25	82	0	63	38	20	25	14	1.91
47316387--47316429	16	2.8	15	79	6	50	44	11	0	44	1.40
47320413--47320442	2	15.5	2	93	6	53	50	0	0	50	1.00
47326292--47326330	20	1.9	21	89	5	62	61	0	2	35	1.10
47328532--47328706	40	4.3	40	81	1	197	23	20	27	29	1.99
47328532--47328706	81	2.2	81	88	4	255	23	20	27	29	1.99
47329066--47329099	14	2.3	15	90	5	52	29	0	32	38	1.58
47329307--47329355	7	7.0	7	83	0	53	24	0	34	40	1.55
47329415--47329490	14	5.3	15	72	9	61	17	1	38	43	1.57
47329415--47329490	7	10.7	7	76	6	55	17	1	38	43	1.57
47329841--47329889	19	2.5	19	90	3	71	75	8	2	14	1.12
47336677--47336713	16	2.3	17	86	13	60	40	0	0	59	0.97
47355417--47355555	51	2.7	51	79	7	158	33	27	15	23	1.95
47357214--47357245	2	16.0	2	93	0	55	46	0	0	53	1.00
47360352--47360377	3	8.7	3	100	0	52	0	30	0	69	0.89
47362934--47362977	22	2.0	23	86	4	63	56	0	0	43	0.99
47362935--47362965	15	2.0	16	93	6	55	61	0	0	38	0.96
47363381--47363435	18	3.0	17	84	10	56	49	3	5	41	1.43
47368522--47368548	11	2.5	11	100	0	54	74	0	25	0	0.83
47369217--47369263	24	2.0	24	84	16	62	31	0	17	51	1.46
47380247--47380275	15	1.9	15	100	0	58	55	0	3	41	1.17
47384825--47384872	3	16.0	3	100	0	96	66	0	0	33	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47385697--47385746	5	10.0	5	75	16	50	58	2	0	40	1.10
47385695--47385747	27	2.0	25	89	7	79	54	1	0	43	1.11
47386393--47386423	9	3.4	9	95	0	53	48	19	6	25	1.72
47392826--47392879	15	3.4	15	75	12	54	9	27	9	53	1.63
47403926--47404015	31	2.9	31	93	0	153	42	12	11	34	1.78
47407385--47407431	22	2.1	22	84	0	58	59	10	2	27	1.42
47428260--47428311	17	2.9	17	80	11	50	57	15	9	17	1.64
47431233--47431531	46	6.6	46	92	1	480	33	15	21	29	1.95
47438953--47439025	27	2.7	28	80	4	69	39	2	9	47	1.50
47447600--47447645	2	23.0	2	100	0	92	50	0	0	50	1.00
47449405--47449448	19	2.3	20	81	14	58	36	2	2	59	1.23
47454053--47454102	20	2.4	21	83	6	75	58	0	2	40	1.10
47454061--47454125	28	2.3	28	89	2	103	56	0	3	40	1.15
47454069--47454174	34	3.3	33	78	18	100	58	0	2	38	1.13
47457540--47457615	36	2.1	37	82	2	91	40	7	0	51	1.31
47465754--47465830	38	2.0	38	100	0	154	32	15	2	49	1.58
47475630--47475669	16	2.5	16	95	0	71	27	27	2	42	1.68
47475835--47475877	2	21.5	2	100	0	86	48	0	0	51	1.00
47475999--47476039	21	2.0	21	85	9	57	70	7	0	21	1.11
47476020--47476067	26	1.9	24	83	8	60	68	8	2	20	1.26
47481769--47481797	2	14.5	2	100	0	58	48	0	0	51	1.00
47482196--47482227	13	2.5	13	95	5	57	25	0	0	75	0.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47483806--47483843	21	1.9	20	89	10	60	10	10	5	73	1.23
47486533--47486610	29	2.6	29	83	4	93	47	14	14	24	1.80
47491390--47491424	17	2.1	17	89	5	54	57	5	0	37	1.23
47494438--47494468	16	1.9	16	93	0	53	38	0	0	61	0.96
47494440--47494472	17	1.9	17	93	0	57	39	0	0	60	0.97
47496331--47496423	32	2.9	31	93	6	159	27	3	17	51	1.60
47497801--47497838	14	2.7	14	88	11	60	44	13	2	39	1.57
47504952--47505035	40	2.1	40	97	0	159	35	23	14	26	1.93
47509753--47509783	14	2.2	14	94	0	53	0	9	3	87	0.66
47510412--47510461	25	2.0	25	100	0	100	36	16	8	40	1.77
47512480--47512510	14	2.2	14	100	0	62	45	0	0	54	0.99
47514298--47514376	41	2.0	40	85	7	106	29	1	5	64	1.22
47516489--47516513	3	8.3	3	100	0	50	0	32	0	68	0.90
47521467--47521524	22	2.8	20	80	12	62	39	3	0	56	1.16
47523516--47523566	21	2.4	21	83	6	59	37	1	17	43	1.61
47524021--47524080	24	2.5	24	88	0	84	15	28	23	33	1.94
47525339--47525386	17	2.9	17	84	3	62	25	2	18	54	1.55
47526602--47526740	46	3.0	46	92	0	224	35	11	24	28	1.90
47527374--47527398	5	5.0	5	100	0	50	80	0	0	20	0.72
47534747--47534807	24	2.5	24	83	0	77	16	24	22	36	1.94
47535885--47535981	49	2.0	48	87	2	140	42	21	14	21	1.88
47539802--47539847	23	2.0	24	86	4	67	67	6	2	23	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47540181--47540248	32	2.2	29	75	17	57	48	5	4	41	1.47
47551997--47552021	2	12.5	2	100	0	50	52	0	0	48	1.00
47560676--47560785	30	3.7	30	96	0	202	54	0	9	36	1.32
47560684--47560810	60	2.1	60	85	5	168	55	0	7	35	1.34
47560778--47560831	23	2.3	23	78	15	58	57	3	1	37	1.27
47561084--47561136	21	2.5	21	87	0	79	30	37	9	22	1.86
47561397--47561477	37	2.1	39	86	6	112	61	13	12	12	1.57
47564016--47564042	11	2.5	11	100	0	54	0	7	22	70	1.12
47564029--47564086	19	2.9	19	75	17	55	0	13	10	75	1.04
47564627--47564691	32	2.1	32	97	2	123	47	12	9	30	1.72
47564780--47564804	3	8.3	3	100	0	50	68	0	0	32	0.90
47569276--47569672	196	2.0	196	81	3	460	33	21	21	23	1.97
47569569--47569664	40	2.4	39	81	6	111	31	22	20	25	1.98
47570494--47570844	9	39.7	9	72	11	201	48	15	0	34	1.52
47570530--47570800	120	2.3	118	77	10	291	47	16	1	34	1.54
47570577--47570855	94	2.9	97	81	10	365	46	16	0	36	1.53
47570700--47570748	22	2.1	23	88	7	73	53	10	2	34	1.47
47572114--47572285	43	4.0	43	77	1	184	25	15	26	32	1.95
47572114--47572277	86	1.9	86	83	7	217	25	15	26	33	1.95
47579569--47579602	2	17.0	2	100	0	68	50	0	0	50	1.00
47579679--47579733	17	3.3	16	82	7	58	38	1	7	52	1.40
47579685--47579733	17	2.8	18	84	9	66	36	2	8	53	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47581071--47581608	294	1.8	288	87	3	801	32	12	10	44	1.76
47582512--47582549	11	3.5	11	88	0	58	31	26	0	42	1.56
47582514--47582563	22	2.3	22	82	0	64	28	24	2	46	1.64
47583630--47583657	11	2.5	11	100	0	56	42	0	32	25	1.55
47586887--47586913	11	2.5	11	100	0	54	25	7	0	66	1.17
47589395--47589442	17	2.9	17	90	3	71	27	0	18	54	1.44
47591440--47591489	24	2.1	24	100	0	100	32	4	14	50	1.61
47591660--47591846	46	4.1	45	86	4	259	36	9	24	29	1.86
47600367--47600410	23	1.9	23	85	0	61	29	2	22	45	1.65
47600367--47600417	23	2.2	23	82	0	57	31	1	21	45	1.63

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