genome.fa.s7.2.7.7.80.10.50.1000.117.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: At_chr3
Parameters: 2 7 7 80 10 50 1000
Length:  100348136

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   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   227   228   229   230   231   232   233   234   235   236   237   238   239   240   
          241   242   243   244   245   246   247   248   249   250   251   252   253   254   255   256   
          257   258   259   260   261   262   263   264   265   266   267   268   269   270   271   272   
          273   274   275   276   277   278   279   280   281   282   283   284   285   286   287   288   
          289   290   

This is table  117  of  290  ( 34714 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)
39879673--39879710	16	2.3	17	90	4	60	76	0	0	23	0.79
39891800--39891849	12	4.8	10	76	23	50	34	0	0	66	0.92
39894234--39894280	18	2.6	18	80	10	51	44	0	12	42	1.42
39894359--39894392	9	3.8	9	88	0	50	41	0	2	55	1.15
39895180--39895231	26	2.0	26	85	14	72	65	0	1	32	1.04
39895743--39895777	19	1.9	19	88	11	56	37	0	0	62	0.95
39897203--39897245	14	2.9	15	79	6	61	69	11	0	18	1.17
39900814--39900856	21	2.0	21	81	9	50	30	6	4	58	1.45
39904131--39904182	19	2.7	19	88	5	70	26	19	5	48	1.71
39915737--39915807	34	2.1	34	97	0	133	21	9	25	43	1.83
39918907--39919020	51	2.2	51	95	0	201	33	14	23	28	1.94
39920874--39921049	44	4.0	44	80	5	167	31	17	22	28	1.97
39920878--39921044	88	1.9	89	83	1	219	30	17	22	29	1.96
39921153--39921389	94	2.5	94	80	2	262	31	18	20	29	1.97
39923955--39924375	182	2.3	183	83	6	517	30	19	11	38	1.87
39924164--39924585	217	1.9	216	91	0	682	29	19	11	39	1.87
39925995--39926048	28	1.9	28	88	0	81	62	1	5	29	1.28
39926160--39926219	24	2.6	23	74	10	59	38	1	3	56	1.26
39929290--39929337	24	2.0	24	92	8	80	77	0	10	12	1.00
39939686--39939853	84	2.0	84	98	0	327	35	18	13	32	1.89
39943777--39943811	7	5.3	7	90	10	56	28	60	0	11	1.32
39947309--39947464	80	2.0	80	96	0	285	40	7	16	35	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39949735--39949787	21	2.5	21	87	0	79	15	18	20	45	1.85
39950799--39950837	20	2.0	20	84	0	51	33	20	2	43	1.65
39951908--39951944	20	1.9	18	89	10	56	43	0	21	35	1.53
39957511--39957573	25	2.4	25	84	5	72	68	1	0	30	0.99
39957720--39957761	8	5.4	8	82	5	59	35	0	2	61	1.09
39957720--39957765	23	2.0	24	87	8	69	39	0	2	58	1.10
39961704--39961747	22	2.0	22	95	0	79	34	11	13	40	1.81
39962922--39962961	19	2.1	19	95	0	71	30	5	32	32	1.79
39964736--39964819	42	2.0	42	95	0	150	38	23	4	33	1.76
39965751--39965850	50	2.0	50	100	0	200	44	18	6	32	1.74
39984162--39984210	3	16.3	3	100	0	98	34	0	0	65	0.93
39984209--39984263	3	18.3	3	100	0	110	32	0	32	34	1.58
39995782--39995816	6	5.8	6	90	10	54	82	0	14	2	0.77
39999110--39999142	14	2.4	14	95	5	59	33	9	27	30	1.88
40011628--40011667	20	2.0	21	90	5	64	32	5	2	60	1.32
40011714--40011747	13	2.7	13	86	4	52	38	0	0	61	0.96
40011719--40011764	20	2.3	20	72	17	51	34	0	0	65	0.93
40012307--40012354	25	1.9	25	82	0	60	60	4	4	31	1.35
40012828--40012890	30	2.1	30	91	5	101	25	4	11	58	1.51
40014971--40015014	16	2.8	16	86	10	56	70	0	0	29	0.88
40015629--40015674	23	2.0	23	100	0	92	30	21	17	30	1.96
40026064--40026284	46	4.8	46	97	0	370	28	28	21	20	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40029398--40029525	41	3.1	41	89	1	193	37	22	21	17	1.94
40029698--40029797	14	6.9	14	70	8	65	29	1	25	45	1.60
40029709--40029790	21	3.7	21	75	12	83	28	1	26	43	1.62
40029713--40029806	46	2.0	46	95	0	170	30	2	24	42	1.66
40030264--40030301	15	2.5	15	95	0	67	39	5	10	44	1.61
40034771--40034813	22	1.9	23	85	4	61	58	4	0	37	1.19
40034854--40034988	43	3.2	43	88	2	191	25	17	28	29	1.97
40034834--40034990	85	1.8	85	86	0	224	25	15	26	32	1.96
40035964--40036028	31	2.1	31	82	2	78	43	10	12	33	1.77
40035974--40036038	31	2.1	30	85	2	85	38	9	13	38	1.77
40036995--40037022	14	2.0	14	100	0	56	35	14	7	42	1.73
40037487--40037618	43	3.1	43	90	1	203	25	20	26	28	1.99
40037677--40037757	31	2.6	31	76	5	65	60	17	4	17	1.53
40037992--40038085	21	4.5	21	80	10	120	0	48	20	30	1.49
40038036--40038086	18	2.8	18	76	8	50	0	50	21	27	1.48
40039021--40039232	106	2.0	106	99	0	415	30	21	9	37	1.86
40042557--40042677	9	13.6	9	69	12	63	33	2	20	42	1.65
40042631--40042862	56	4.2	56	89	5	348	34	0	16	48	1.50
40042631--40042841	113	1.9	112	93	3	361	33	0	17	48	1.51
40042787--40042816	13	2.3	13	100	0	60	36	0	10	53	1.35
40042819--40042849	9	3.4	9	90	0	53	29	0	19	51	1.47
40043256--40043346	36	2.5	37	75	22	104	51	2	9	36	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40045234--40045363	59	2.2	59	87	0	179	36	2	39	21	1.66
40045432--40045970	114	4.7	116	82	6	517	35	23	15	25	1.94
40046836--40046876	7	5.6	7	83	11	55	12	0	34	53	1.38
40046836--40046882	14	3.0	16	87	9	62	12	0	38	48	1.41
40046836--40046884	16	3.2	15	86	11	64	12	0	36	51	1.40
40046845--40046930	45	1.9	45	88	4	129	15	0	34	50	1.44
40046937--40047186	41	6.1	41	80	6	204	19	20	21	38	1.93
40062132--40062214	41	2.0	41	92	0	139	30	25	19	25	1.98
40063228--40063344	62	1.9	59	86	5	162	48	3	5	42	1.42
40063323--40063371	20	2.7	18	77	22	57	51	2	2	44	1.24
40066469--40066568	32	3.0	32	70	15	78	46	7	3	44	1.46
40066476--40066603	69	1.9	68	88	1	193	47	6	3	42	1.47
40070299--40070330	12	2.7	12	95	0	55	25	40	18	15	1.90
40098778--40098812	17	2.1	17	94	0	61	48	14	11	25	1.77
40100191--40100230	19	2.1	19	90	9	64	60	0	0	40	0.97
40100191--40100230	10	4.2	10	93	6	66	60	0	0	40	0.97
40101820--40101866	24	2.0	24	83	8	60	8	14	29	46	1.74
40103794--40103839	3	15.3	3	100	0	92	32	0	0	67	0.91
40105868--40105908	22	1.9	22	90	5	66	65	0	2	31	1.05
40106108--40106151	19	2.2	20	84	8	54	63	2	2	31	1.19
40113828--40113909	21	4.0	21	80	12	82	42	1	1	54	1.15
40114640--40114689	5	9.8	5	85	10	66	44	0	0	56	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40115860--40117736	938	2.0	938	100	0	3754	37	10	20	31	1.86
40117825--40117893	34	2.0	34	100	0	138	42	2	31	23	1.69
40126841--40126944	31	3.4	30	74	15	90	37	1	6	53	1.38
40134568--40134659	46	2.0	46	93	4	159	27	8	25	39	1.85
40144935--40145020	42	2.0	42	93	0	145	31	23	16	29	1.96
40145232--40145412	92	2.0	92	88	2	274	23	17	22	37	1.94
40151084--40151207	46	2.7	46	92	2	196	40	13	23	22	1.90
40151308--40151337	13	2.3	13	94	0	51	36	0	26	36	1.57
40151505--40151537	17	2.0	17	88	5	50	51	0	12	36	1.39
40172943--40172969	2	13.5	2	100	0	54	48	0	0	51	1.00
40181773--40181829	21	2.6	22	81	15	66	29	1	1	66	1.12
40181773--40181822	9	4.8	10	79	20	50	32	0	2	66	1.03
40182200--40182490	146	2.0	146	82	2	352	36	15	21	26	1.93
40183078--40183122	23	2.0	23	95	0	81	26	11	15	46	1.79
40186644--40186673	12	2.5	12	88	0	51	56	3	0	40	1.16
40187637--40187950	91	3.5	89	78	13	306	39	19	8	33	1.81
40187637--40187956	178	1.8	177	84	4	439	39	19	8	32	1.82
40188035--40188137	10	10.5	10	71	12	79	68	0	4	26	1.09
40188034--40188098	11	6.5	11	77	13	54	76	0	3	20	0.91
40188043--40188068	8	3.2	8	100	0	52	84	0	0	15	0.62
40188034--40188087	27	2.0	28	88	3	83	77	0	1	20	0.86
40188031--40188120	21	4.7	19	74	15	69	70	0	5	24	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40188093--40188137	21	2.2	20	88	4	63	62	0	6	31	1.21
40188108--40188146	19	2.0	20	85	5	53	56	2	2	38	1.27
40188329--40188367	20	2.0	20	89	0	60	28	2	2	66	1.18
40188388--40188516	10	13.5	10	68	18	53	31	2	0	65	1.11
40188387--40188457	19	3.8	18	77	17	74	30	2	0	66	1.06
40188379--40188469	19	4.8	19	72	11	62	36	2	0	61	1.08
40188426--40188497	29	2.5	29	80	6	85	37	1	1	59	1.15
40188388--40188514	9	13.4	9	71	16	62	31	2	0	65	1.11
40188576--40188759	91	2.0	91	82	6	221	33	7	19	39	1.80
40188931--40188956	6	4.3	6	100	0	52	30	0	0	69	0.89

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   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   227   228   229   230   231   232   233   234   235   236   237   238   239   240   
          241   242   243   244   245   246   247   248   249   250   251   252   253   254   255   256   
          257   258   259   260   261   262   263   264   265   266   267   268   269   270   271   272   
          273   274   275   276   277   278   279   280   281   282   283   284   285   286   287   288   
          289   290