genome.fa.s2.2.7.7.80.10.50.1000.16.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: At_chr1
Parameters: 2 7 7 80 10 50 1000
Length:  106989029

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   291   292   293   294   295   296   297   298   299   300   301   302   303   304   
          305   306   307   308   309   310   311   312   313   314   315   316   317   318   319   320   
          321   322   

This is table  16  of  322  ( 38559 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)
4426488--4426548	19	3.2	19	79	9	70	34	0	13	52	1.40
4426497--4426553	19	2.9	19	86	2	78	33	0	14	52	1.41
4426493--4426658	41	4.1	40	74	17	171	33	0	12	54	1.38
4426611--4427207	97	6.1	97	98	0	1113	30	1	13	55	1.45
4427144--4427201	22	2.9	19	71	14	53	34	1	12	51	1.49
4430407--4430471	6	10.8	6	91	0	103	0	36	30	32	1.58
4432094--4432135	16	2.7	15	85	7	57	57	2	2	38	1.25
4432246--4432319	38	1.9	38	94	0	130	40	2	4	52	1.34
4432595--4432756	20	7.9	22	71	16	93	54	12	0	32	1.39
4432594--4432755	40	4.0	39	74	17	161	54	12	0	32	1.39
4432594--4432652	18	3.1	18	83	11	73	52	13	0	33	1.41
4432536--4432758	19	11.5	19	66	22	108	53	13	0	33	1.43
4433288--4433326	21	1.9	20	84	5	51	53	5	2	38	1.37
4438682--4438720	13	2.9	13	80	3	51	10	7	2	79	1.02
4446999--4447041	3	14.0	3	95	4	77	65	0	0	34	0.93
4452378--4452470	20	4.8	19	76	7	80	22	1	8	67	1.24
4457120--4457163	23	1.9	23	95	0	79	22	15	15	45	1.85
4464683--4464765	42	2.0	42	83	4	105	40	7	19	32	1.79
4465761--4465814	23	2.3	24	78	9	58	35	1	11	51	1.48
4471777--4472248	235	2.0	235	93	0	811	30	13	22	32	1.93
4472828--4472875	25	1.9	25	87	8	71	33	0	12	54	1.38
4476619--4476678	29	2.1	28	87	3	84	23	11	20	45	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4480336--4480369	13	2.5	13	90	4	50	14	5	5	73	1.21
4483429--4483524	39	2.4	41	79	6	108	41	20	18	18	1.90
4483557--4483754	41	4.9	41	91	1	281	25	21	24	28	1.99
4483581--4483754	81	2.1	81	92	1	285	24	22	25	27	2.00
4483848--4483898	26	2.0	26	88	0	75	60	5	9	23	1.50
4484244--4484373	62	2.1	63	84	4	165	27	1	25	45	1.62
4484515--4484562	21	2.3	21	76	16	55	37	0	33	29	1.58
4489703--4489775	35	2.1	36	84	7	96	35	1	5	57	1.30
4489908--4490226	43	7.5	42	77	7	119	24	17	25	32	1.97
4489982--4490229	43	5.8	43	79	2	248	26	19	25	29	1.98
4489961--4490233	86	3.2	86	84	1	323	24	19	24	30	1.98
4493623--4493652	15	2.0	15	93	0	51	36	13	13	36	1.84
4500511--4500566	9	6.2	9	80	0	67	23	25	16	35	1.94
4509271--4509326	27	2.1	27	93	0	94	41	16	7	35	1.75
4509271--4509311	13	3.0	14	73	20	50	43	14	4	36	1.67
4509273--4509320	15	3.4	15	72	16	57	41	18	2	37	1.63
4512075--4512104	9	3.3	9	90	0	51	26	20	23	30	1.98
4519897--4519926	15	1.9	16	93	6	53	30	0	30	40	1.57
4525039--4525172	61	2.2	60	89	1	196	30	29	24	14	1.95
4525153--4525367	43	5.5	42	72	20	214	34	27	16	21	1.95
4525187--4525400	33	5.8	33	70	22	133	35	27	18	18	1.94
4525151--4525402	76	3.3	76	92	3	409	34	28	17	19	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4529315--4529341	13	2.1	13	100	0	54	33	14	7	44	1.73
4529892--4529940	25	2.0	25	84	8	64	34	16	30	18	1.93
4534304--4534346	18	2.4	18	92	7	70	55	0	0	44	0.99
4534429--4534457	13	2.2	13	100	0	58	31	17	20	31	1.96
4537846--4537893	25	1.9	25	91	8	80	33	0	14	52	1.42
4541685--4541727	18	2.4	18	88	7	61	53	0	0	46	1.00
4546940--4547333	153	2.6	153	85	4	528	25	19	17	37	1.93
4551951--4551989	16	2.4	16	91	0	60	53	10	0	35	1.35
4551993--4552034	16	2.6	16	92	0	66	42	7	2	47	1.43
4559651--4559676	5	5.2	5	100	0	52	19	0	0	80	0.71
4581070--4581269	100	2.0	100	98	0	382	42	18	11	27	1.85
4582837--4582875	16	2.6	15	88	8	53	35	0	2	61	1.10
4591562--4591627	33	2.0	33	100	0	132	27	15	27	30	1.96
4596056--4596087	7	4.7	7	96	3	57	37	0	0	62	0.95
4596048--4596087	13	3.0	13	89	7	62	37	0	0	62	0.95
4596048--4596087	20	2.0	20	85	9	55	37	0	0	62	0.95
4597986--4598037	26	2.0	26	100	0	104	57	3	11	26	1.51
4597988--4598044	26	2.2	26	93	0	96	57	7	8	26	1.54
4598305--4598355	18	2.9	18	80	11	52	37	1	0	60	1.08
4603646--4604011	153	2.4	153	89	2	549	26	19	16	37	1.93
4603646--4604064	153	2.7	152	85	3	475	25	20	15	37	1.93
4609690--4609715	5	5.2	5	100	0	52	19	0	0	80	0.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4613984--4614025	20	2.1	20	100	0	84	33	23	4	38	1.76
4617550--4617617	21	3.2	20	69	19	57	42	20	13	23	1.87
4617529--4617627	43	2.3	43	85	3	146	41	16	15	27	1.88
4617548--4617615	22	3.1	21	68	19	59	44	20	11	23	1.84
4620192--4620233	3	14.0	3	85	9	59	0	35	0	64	0.94
4620193--4620286	12	8.1	12	75	10	52	7	39	1	52	1.37
4626512--4626571	29	2.1	29	100	0	120	43	3	20	33	1.68
4632158--4632192	16	2.2	16	89	0	52	40	20	14	25	1.90
4632089--4632295	103	2.0	100	88	4	308	42	14	16	25	1.87
4633652--4633690	20	2.0	20	89	0	60	51	17	5	25	1.66
4636269--4636301	10	3.5	10	84	16	52	30	0	18	51	1.46
4641737--4641774	14	2.7	14	87	0	58	65	15	5	13	1.43
4641783--4641835	22	2.4	23	84	12	67	67	7	9	15	1.39
4641792--4641852	31	1.9	31	83	6	77	70	6	11	11	1.33
4641783--4641851	22	3.1	22	74	15	54	71	5	10	13	1.31
4644731--4644858	41	3.1	40	77	9	116	30	25	17	25	1.98
4645876--4645951	9	8.4	9	85	5	100	23	9	22	44	1.81
4648587--4648627	3	13.7	3	100	0	82	34	0	0	65	0.93
4653619--4653646	14	2.0	14	100	0	56	28	14	14	42	1.84
4659027--4659061	16	2.2	16	89	0	52	8	20	0	71	1.11
4661530--4661570	16	2.6	17	85	14	54	24	0	9	65	1.22
4662064--4662106	21	2.0	21	81	0	50	53	0	0	46	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4669995--4670047	20	2.7	20	85	5	72	45	7	3	43	1.50
4689399--4689430	12	2.6	13	90	9	50	0	6	6	87	0.67
4690674--4690716	18	2.4	19	84	7	54	48	0	6	44	1.29
4696342--4696380	18	2.2	18	90	0	60	41	41	0	17	1.50
4696530--4696604	37	2.0	37	97	0	141	33	6	16	44	1.73
4696539--4696595	17	3.2	17	67	13	51	31	3	15	49	1.62
4696603--4696642	9	4.4	9	83	0	53	30	10	17	42	1.82
4704575--4704636	24	2.7	22	80	9	79	32	3	4	59	1.34
4704575--4704696	23	5.2	23	70	9	86	32	8	3	55	1.45
4704729--4704796	33	2.1	33	97	0	127	39	16	8	35	1.79
4704798--4704856	24	2.4	23	77	22	59	35	1	3	59	1.24
4706146--4706175	14	2.1	14	93	0	51	46	6	6	40	1.56
4708094--4708119	6	4.3	6	100	0	52	50	0	0	50	1.00
4711260--4711299	13	3.4	12	90	10	57	20	0	0	80	0.72
4711269--4711304	13	2.7	13	86	4	54	22	0	0	77	0.76
4714490--4714523	5	6.8	5	93	0	50	76	0	5	17	0.98
4715714--4715764	20	2.5	20	87	12	70	33	0	7	58	1.27
4717492--4717539	24	2.0	24	84	8	62	77	2	4	16	1.03
4723338--4723450	44	2.6	44	81	12	135	28	21	24	25	1.99
4727073--4727391	36	8.0	36	71	19	215	28	20	13	37	1.91
4727109--4727427	46	7.6	46	73	19	329	28	21	12	37	1.90
4727030--4727427	82	4.9	82	96	0	703	28	21	13	36	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4727885--4727912	13	2.2	13	100	0	56	35	42	0	21	1.53
4729240--4729280	21	2.0	21	95	0	73	19	9	36	34	1.85
4733169--4733288	61	2.0	60	93	1	204	28	23	25	23	2.00
4750274--4750299	3	8.7	3	100	0	52	30	0	0	69	0.89
4753824--4754280	247	1.8	252	90	3	753	32	11	12	43	1.78
4761550--4761722	88	2.0	88	85	4	233	34	13	9	42	1.78
4764153--4764230	30	2.5	31	81	10	88	48	2	1	47	1.23
4766364--4766393	15	2.1	15	93	6	53	43	13	0	43	1.43
4774339--4774379	20	2.0	20	100	0	82	9	14	19	56	1.66
4774345--4774388	20	2.2	20	84	4	54	18	11	18	52	1.74

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   291   292   293   294   295   296   297   298   299   300   301   302   303   304   
          305   306   307   308   309   310   311   312   313   314   315   316   317   318   319   320   
          321   322