genome.fa.s25.2.7.7.80.10.50.1000.13.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_chr12
Parameters: 2 7 7 80 10 50 1000
Length:  101062743

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   

This is table  13  of  297  ( 35593 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)
4104184--4104428	52	4.9	50	70	20	156	33	2	1	62	1.18
4104137--4104387	80	3.1	78	74	14	203	32	2	1	63	1.17
4104712--4104761	26	1.9	26	83	0	64	36	4	0	60	1.16
4110954--4111135	40	4.6	40	83	0	229	18	21	28	31	1.97
4112626--4112656	15	2.1	15	100	0	62	19	51	0	29	1.47
4119234--4119351	58	2.0	58	98	0	227	27	18	16	38	1.92
4126225--4126262	19	2.0	19	94	0	67	13	18	21	47	1.82
4141855--4141923	34	2.0	34	97	0	129	50	0	18	30	1.47
4145302--4145340	12	3.2	12	92	3	60	2	7	2	87	0.73
4147931--4147973	19	2.2	21	88	12	65	55	0	2	41	1.12
4147967--4148032	19	3.5	18	76	15	62	37	0	1	60	1.06
4147977--4148038	20	3.1	21	82	15	71	41	0	1	56	1.09
4147993--4148045	20	2.7	21	82	11	58	49	0	0	50	1.00
4149033--4149061	14	2.0	15	93	6	51	13	17	6	62	1.52
4151373--4151401	14	2.0	15	93	6	51	20	6	6	65	1.40
4155220--4156212	40	24.9	40	98	0	1891	29	29	17	22	1.97
4156192--4156232	20	2.0	20	100	0	82	34	36	14	14	1.87
4156152--4156272	60	2.0	60	100	0	242	29	32	18	19	1.96
4156212--4156420	40	5.2	40	93	2	341	28	28	19	23	1.98
4156112--4156312	100	2.0	100	98	0	384	29	31	17	20	1.96
4156072--4156352	140	2.0	140	98	0	544	29	30	18	21	1.97
4156032--4156382	180	2.0	180	98	0	675	29	30	18	22	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4155992--4156420	220	2.0	220	94	1	763	29	29	18	22	1.98
4165125--4165435	46	6.7	46	96	0	559	20	19	28	30	1.97
4171923--4171953	5	6.2	5	92	0	53	41	3	19	35	1.67
4171925--4171955	15	2.1	15	100	0	62	41	6	19	32	1.77
4173464--4173506	22	2.0	22	95	0	77	44	9	30	16	1.79
4174993--4175023	6	5.2	6	100	0	62	0	0	32	67	0.91
4176620--4176747	66	1.9	68	88	3	197	33	13	20	32	1.91
4178588--4178612	3	8.3	3	100	0	50	32	0	0	68	0.90
4179811--4179882	36	2.0	36	100	0	144	38	13	16	30	1.88
4180407--4180431	13	1.9	13	100	0	50	48	40	12	0	1.40
4181804--4181869	27	2.5	25	78	11	69	24	7	1	66	1.26
4182088--4182218	26	5.1	25	72	14	88	31	5	4	58	1.40
4186290--4186339	13	3.9	13	84	2	66	34	2	8	56	1.40
4190567--4190625	10	5.9	10	85	0	73	66	0	10	23	1.22
4192829--4192872	17	2.5	18	81	7	54	31	15	9	43	1.79
4193753--4193888	3	45.3	3	100	0	272	66	0	0	33	0.92
4200498--4200539	22	1.9	22	85	9	59	69	4	2	23	1.20
4200507--4200549	22	2.0	21	86	4	59	67	4	4	23	1.28
4201583--4201614	10	3.1	11	86	13	50	9	18	18	53	1.71
4201839--4201877	17	2.3	17	86	8	53	12	0	7	79	0.93
4201830--4201876	23	2.0	23	83	0	58	12	0	8	78	0.95
4212685--4212737	21	2.7	20	80	8	54	15	5	7	71	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4212685--4212737	20	2.6	20	77	11	54	15	5	7	71	1.27
4219768--4219798	4	8.0	4	92	7	55	51	0	0	48	1.00
4224489--4224558	27	2.6	27	95	2	113	31	28	12	27	1.93
4224489--4224586	28	3.5	28	90	2	135	31	28	13	26	1.94
4225884--4226041	79	2.0	79	98	0	307	30	23	13	32	1.94
4232895--4232935	17	2.4	17	100	0	82	4	26	46	21	1.72
4237494--4237623	65	2.0	65	87	0	188	36	14	36	13	1.85
4245145--4245232	29	3.1	28	85	8	115	26	15	26	31	1.96
4249194--4249266	29	2.6	29	88	2	112	23	16	30	30	1.96
4258402--4258642	40	6.1	40	88	0	340	25	28	21	24	1.99
4258696--4258770	38	2.0	38	86	0	105	25	26	18	29	1.98
4259693--4259778	43	2.0	43	93	0	145	32	15	20	31	1.94
4265132--4265206	38	2.0	38	91	0	123	21	22	26	29	1.99
4265183--4265367	43	4.3	43	87	1	248	14	23	31	30	1.94
4268555--4268614	30	2.0	30	84	12	79	13	10	13	63	1.52
4270758--4270950	50	3.9	49	79	8	203	26	18	27	27	1.98
4282639--4282682	17	2.5	18	81	7	54	45	11	20	22	1.83
4282665--4282694	12	2.4	12	94	5	51	46	10	20	23	1.80
4282628--4282709	30	2.5	32	76	9	87	47	13	18	20	1.82
4283055--4283394	27	12.8	27	86	5	408	39	20	14	25	1.90
4284685--4284720	18	2.0	18	94	0	63	38	36	5	19	1.75
4290377--4290455	37	2.1	37	88	0	113	22	20	31	25	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4294362--4294398	20	1.9	18	89	10	56	43	0	21	35	1.53
4327365--4327645	48	5.9	48	74	9	229	23	28	19	28	1.98
4329230--4329289	24	2.4	25	79	17	72	25	11	20	43	1.85
4346795--4347077	40	7.1	40	96	1	507	27	26	22	22	1.99
4352086--4352258	46	3.7	46	78	13	210	21	21	27	28	1.99
4352083--4352253	93	1.8	93	96	0	315	21	21	28	28	1.99
4359674--4359846	46	3.7	46	80	13	228	21	20	28	29	1.98
4359671--4359841	93	1.8	93	97	0	324	21	21	29	28	1.98
4369390--4369505	48	2.4	48	85	0	151	27	21	21	29	1.99
4369262--4369724	250	1.9	250	89	0	730	28	14	24	32	1.95
4376672--4376737	34	1.9	34	81	6	80	28	1	28	40	1.65
4377176--4377354	85	2.1	85	100	0	358	37	8	27	26	1.85
4378805--4378989	40	4.6	40	84	0	244	25	24	25	23	2.00
4385101--4385278	27	6.6	27	83	3	205	26	15	28	29	1.96
4385102--4385257	82	1.9	81	88	3	233	26	15	28	29	1.96
4385098--4385278	82	2.2	81	83	2	229	27	15	27	29	1.96
4391770--4392016	40	6.2	40	84	5	272	23	24	27	24	2.00
4391770--4391993	119	1.9	120	84	2	308	22	24	28	24	2.00
4391810--4392016	79	2.6	78	85	5	263	23	24	27	24	2.00
4391810--4392026	119	1.8	119	83	4	287	23	24	27	23	2.00
4403205--4403361	43	3.7	42	77	12	167	24	16	25	33	1.96
4407198--4407312	29	4.0	29	77	6	101	29	26	16	27	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4407371--4407416	18	2.6	18	82	6	58	21	34	23	19	1.96
4407527--4407567	16	2.6	16	84	0	55	9	17	21	51	1.74
4424162--4424276	29	4.0	29	83	6	137	27	28	15	27	1.96
4428787--4428938	76	2.0	76	98	0	295	30	24	5	39	1.77
4429315--4429384	28	2.5	28	80	0	77	28	27	8	35	1.86
4436063--4436122	28	2.2	26	80	11	75	26	25	11	36	1.90
4436077--4436144	28	2.4	28	92	0	109	27	25	14	32	1.95
4440485--4440602	46	2.6	46	88	0	164	33	13	23	28	1.93
4468200--4468241	18	2.3	18	80	8	50	30	0	26	42	1.55
4475356--4475388	14	2.5	13	90	9	57	12	15	12	60	1.59
4478189--4478221	16	2.1	16	100	0	66	12	24	12	51	1.73
4478547--4478580	17	1.9	18	88	5	52	55	26	11	5	1.58
4487269--4487311	15	2.9	14	81	18	52	72	0	0	27	0.85
4487269--4487311	12	3.4	13	81	15	54	72	0	0	27	0.85
4490930--4490968	19	2.1	19	95	0	69	15	12	25	46	1.81
4493165--4493387	39	5.7	40	85	8	266	25	22	27	24	2.00
4493165--4493387	79	2.8	81	84	9	282	25	22	27	24	2.00
4493165--4493420	79	3.3	79	81	10	217	26	21	27	24	1.99
4501071--4501255	79	2.3	81	84	7	236	24	22	27	25	2.00
4501072--4501255	40	4.6	40	83	9	216	24	22	27	25	2.00
4501072--4501288	79	2.7	79	81	7	201	25	22	27	24	2.00
4520735--4520795	30	2.0	30	83	0	77	31	22	8	37	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4528085--4528206	47	2.6	47	93	0	199	36	14	22	26	1.93
4528185--4528643	53	8.6	54	78	8	415	35	17	23	23	1.95
4528179--4528655	162	3.0	159	74	8	443	35	17	23	23	1.95
4528132--4528655	262	2.0	262	93	0	897	35	16	23	23	1.95
4556824--4557031	28	7.6	27	93	3	326	25	14	28	31	1.95
4556824--4557031	55	3.8	55	93	1	344	25	14	28	31	1.95
4556824--4557031	83	2.5	83	92	2	346	25	14	28	31	1.95
4560311--4560450	47	3.0	47	90	0	226	28	14	12	44	1.82
4561255--4561468	45	4.9	45	84	6	214	25	20	28	25	1.99
4561956--4561988	16	1.9	18	88	11	52	24	15	12	48	1.78

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