genome.fa.s8.2.7.7.80.10.50.1000.144.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  144  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)
42422200--42422238	18	2.1	18	90	4	60	41	0	33	25	1.56
42422183--42422245	21	3.1	20	78	17	76	44	0	33	22	1.53
42422610--42422646	9	4.1	9	92	0	65	29	10	13	45	1.77
42422702--42422738	9	4.1	9	92	0	65	43	21	10	24	1.84
42432661--42432729	38	1.9	37	85	11	99	39	5	0	55	1.24
42440219--42440256	18	2.1	18	85	9	51	15	15	7	60	1.57
42440244--42440344	12	7.9	12	70	14	69	24	12	9	52	1.70
42440287--42440355	24	2.8	24	80	10	77	27	11	10	50	1.70
42440251--42440368	25	4.7	24	76	12	94	24	14	8	52	1.69
42441659--42441693	6	5.8	6	96	0	61	82	0	14	2	0.77
42441718--42442208	246	2.0	246	97	0	939	40	6	15	36	1.75
42449298--42449604	103	3.0	103	90	2	485	20	19	28	32	1.96
42449405--42449631	33	6.5	33	70	22	142	20	19	27	32	1.97
42449475--42449528	27	2.0	28	96	3	101	20	24	29	25	1.99
42458216--42458853	344	1.8	345	94	0	1125	29	8	21	39	1.83
42460609--42460652	23	1.9	23	86	9	63	52	13	4	29	1.60
42460721--42460754	14	2.4	14	90	0	50	64	5	5	23	1.38
42461685--42461815	33	4.0	33	87	0	181	19	24	16	40	1.90
42468825--42468873	26	1.9	26	88	12	75	61	4	2	32	1.26
42477371--42477429	21	2.8	20	80	10	66	27	3	6	62	1.36
42481097--42481123	14	1.9	14	100	0	54	22	7	0	70	1.12
42507445--42507616	53	3.3	50	80	12	179	22	11	3	63	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42511104--42511144	10	4.1	10	77	22	50	31	17	0	51	1.46
42513215--42513261	19	2.5	19	75	6	51	59	10	12	17	1.60
42514228--42514258	6	5.2	6	100	0	62	0	51	0	48	1.00
42519604--42519630	3	9.0	3	100	0	54	33	0	0	66	0.92
42521378--42521407	3	10.0	3	92	0	51	63	3	0	33	1.11
42525117--42525160	19	2.4	18	82	17	56	56	2	6	34	1.38
42531370--42531579	105	2.0	105	100	0	420	32	15	16	36	1.90
42543713--42543755	11	3.8	11	80	17	52	65	2	2	30	1.18
42544583--42544660	10	7.5	10	74	7	57	61	3	3	30	1.32
42544978--42545057	30	2.6	30	79	13	83	37	6	0	56	1.25
42548220--42548280	29	2.0	29	81	6	68	22	16	19	40	1.90
42553404--42553442	19	2.0	19	90	5	60	2	17	0	79	0.84
42568428--42568561	66	2.0	68	89	5	211	20	11	19	48	1.79
42573393--42573422	3	10.0	3	100	0	60	66	0	33	0	0.92
42574485--42574526	11	3.8	11	81	12	50	73	0	2	23	0.94
42574508--42574569	27	2.3	27	86	5	81	66	0	1	32	1.02
42577818--42577902	36	2.3	38	84	11	106	42	2	2	52	1.27
42577936--42577987	26	2.0	26	85	3	70	48	5	0	46	1.26
42579733--42579779	16	2.9	16	77	0	58	27	27	4	40	1.75
42580307--42580332	10	2.6	10	100	0	52	30	19	30	19	1.96
42580612--42580661	20	2.7	18	82	11	73	0	28	26	46	1.53
42580612--42580670	20	3.1	19	77	15	68	0	30	23	45	1.53
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42580569--42580675	26	4.5	25	72	20	86	0	32	19	46	1.56
42580731--42580764	17	2.0	17	100	0	68	11	11	29	47	1.76
42583584--42583612	3	9.7	3	100	0	58	68	0	0	31	0.89
42584849--42584908	25	2.3	27	82	8	79	40	1	3	55	1.27
42592070--42592110	20	2.0	21	85	4	57	41	0	12	46	1.41
42604877--42604929	25	2.1	25	89	6	81	26	22	18	32	1.97
42611243--42611605	199	1.8	199	84	0	501	37	14	19	28	1.91
42612854--42612904	13	3.9	13	77	10	59	37	0	1	60	1.08
42613017--42613047	11	2.8	11	90	0	53	25	0	6	67	1.14
42613704--42613799	39	2.5	38	80	6	106	20	23	29	26	1.99
42613663--42613796	39	3.4	38	72	12	103	21	20	29	28	1.98
42619752--42619804	16	3.3	16	76	10	63	35	24	5	33	1.79
42620023--42620125	37	2.6	39	83	6	129	36	24	15	23	1.93
42620258--42620323	2	33.0	2	100	0	132	50	50	0	0	1.00
42622544--42622581	3	12.7	3	100	0	76	65	0	0	34	0.93
42630607--42630634	13	2.2	13	100	0	56	7	28	14	50	1.69
42633595--42633727	55	2.4	55	82	3	151	26	26	23	24	2.00
42640222--42640470	50	4.8	50	84	4	291	20	28	23	26	1.99
42640221--42640470	100	2.4	104	87	5	346	20	28	23	26	1.99
42656506--42656544	16	2.4	17	83	16	55	66	0	0	33	0.92
42656484--42656544	24	2.5	24	83	2	68	63	0	3	32	1.10
42660213--42660350	72	2.0	68	87	5	195	48	5	3	42	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42660213--42660317	36	2.9	36	72	10	106	49	6	1	41	1.40
42660222--42660369	68	2.1	71	80	7	160	50	4	3	42	1.38
42665071--42665182	21	5.3	21	75	4	100	12	24	16	46	1.82
42665069--42665179	42	2.6	43	78	7	111	12	25	16	45	1.82
42668057--42668175	52	2.3	52	86	9	165	42	5	22	29	1.77
42669084--42669129	22	2.1	22	84	8	58	52	13	6	28	1.65
42669362--42669388	10	2.7	10	100	0	54	70	0	0	29	0.88
42670975--42671025	18	2.8	18	84	0	75	13	37	29	19	1.90
42675196--42675234	20	2.0	20	94	0	69	15	23	7	53	1.67
42685202--42685253	22	2.4	22	93	3	88	46	1	25	26	1.63
42685630--42685667	10	3.5	11	86	13	53	34	0	2	63	1.09
42688789--42688863	33	2.3	33	95	0	132	46	2	13	37	1.57
42689430--42689483	23	2.3	23	83	0	63	62	0	0	37	0.95
42689667--42689744	24	3.3	22	71	18	59	56	1	1	41	1.15
42696650--42696680	16	1.9	16	100	0	62	19	12	29	38	1.89
42702699--42702731	15	2.3	15	89	5	50	75	0	6	18	1.00
42704530--42704918	44	8.6	45	79	8	373	28	19	18	33	1.96
42704530--42704918	89	4.3	88	78	11	342	28	19	18	33	1.96
42709276--42709351	25	3.2	25	73	17	90	46	39	2	11	1.55
42711752--42711785	16	2.2	15	94	5	59	64	0	8	26	1.22
42712610--42712731	61	2.0	61	100	0	244	26	24	21	27	1.99
42719647--42719686	20	2.0	20	85	9	55	22	30	0	47	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42722989--42723022	18	1.9	18	94	5	61	61	2	5	29	1.34
42723043--42723088	24	1.9	24	86	8	67	67	6	2	23	1.25
42724008--42724066	27	2.2	27	81	6	75	44	0	1	54	1.10
42724278--42724344	29	2.3	28	84	5	80	28	16	14	40	1.88
42724566--42724843	125	2.2	124	89	3	425	30	15	22	31	1.95
42725725--42725842	29	4.0	30	84	4	152	34	24	3	37	1.72
42725777--42725857	29	2.8	28	77	9	81	35	23	7	33	1.83
42726179--42726245	10	6.4	10	72	14	55	74	4	19	1	1.07
42726355--42726438	4	20.8	4	79	16	93	77	0	22	0	0.77
42726352--42726444	27	3.3	26	79	16	89	77	0	22	0	0.77
42726359--42726438	23	3.7	23	79	14	98	77	0	22	0	0.77
42726335--42726431	41	2.4	40	81	11	108	74	0	24	1	0.89
42726352--42726438	19	4.9	17	76	20	90	77	0	22	0	0.78
42726471--42726499	10	2.7	11	94	5	51	17	58	20	3	1.53
42726739--42726815	7	11.0	7	78	13	79	79	1	19	0	0.81
42726749--42726815	8	8.4	8	77	9	66	80	0	19	0	0.71
42726742--42726815	13	5.2	15	73	16	68	79	1	18	0	0.80
42726756--42726810	18	3.2	18	76	21	55	80	0	20	0	0.72
42726751--42726820	20	3.5	20	75	18	65	80	0	20	0	0.72
42726739--42726822	26	3.4	25	85	12	111	77	1	21	0	0.84
42726959--42727005	22	2.1	23	84	11	62	34	4	0	61	1.15
42727124--42727159	17	2.2	16	90	9	56	27	11	11	50	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42727274--42727315	18	2.4	18	84	4	50	28	9	14	47	1.75
42727283--42727458	18	9.3	18	68	18	90	34	13	8	43	1.75
42727358--42727459	21	5.1	21	68	23	78	35	12	7	44	1.72
42727275--42727419	56	2.6	56	78	8	150	32	13	10	43	1.78
42727359--42727499	39	3.6	39	82	11	182	34	12	9	43	1.76
42727281--42727499	77	2.9	77	81	11	231	33	13	9	42	1.77
42727340--42727510	38	4.4	38	79	13	190	32	14	10	42	1.80
42734650--42734676	14	1.9	14	100	0	54	29	7	0	62	1.22
42734678--42736069	76	18.2	74	88	6	1641	26	16	21	35	1.94
42734677--42736069	154	9.1	151	89	5	1826	26	16	21	35	1.94

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