genome.fa.s5.2.7.7.80.10.50.1000.89.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: A05
Parameters: 2 7 7 80 10 50 1000
Length:  100714657

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   

This is table  89  of  318  ( 38109 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)
29923632--29923789	44	3.6	42	75	7	136	31	22	17	28	1.97
29927654--29927684	15	2.1	15	93	0	53	64	0	35	0	0.94
29928147--29928242	27	3.4	28	73	15	74	21	7	32	38	1.81
29934063--29934111	13	3.8	13	77	20	50	69	0	8	22	1.14
29934164--29934342	3	60.0	3	72	11	109	61	2	6	30	1.32
29934128--29934278	72	2.1	72	82	8	191	64	3	5	26	1.30
29935713--29935752	20	2.0	20	85	5	53	30	2	12	55	1.50
29940981--29941054	24	3.1	24	76	7	71	51	6	5	36	1.51
29942554--29942621	32	2.2	32	94	2	120	51	22	11	14	1.74
29942912--29942943	16	2.0	16	100	0	64	25	0	18	56	1.42
29944212--29944267	20	2.8	20	66	12	53	42	25	7	25	1.80
29945022--29945048	13	2.1	13	100	0	54	29	29	0	40	1.57
29947831--29947945	32	3.5	33	76	8	99	32	23	11	33	1.90
29952899--29952942	20	2.2	20	95	0	79	22	45	22	9	1.80
29957643--29957756	33	3.5	33	78	7	115	34	22	10	32	1.88
29962958--29963001	22	2.0	22	100	0	88	22	13	9	54	1.67
29968874--29968940	35	1.9	35	87	3	100	32	10	13	43	1.78
29972735--29972774	13	3.0	13	89	10	55	57	0	0	42	0.98
29972737--29972774	14	2.7	14	88	12	60	55	0	0	44	0.99
29976901--29976950	23	2.1	23	85	7	64	40	0	2	58	1.10
29982457--29982540	31	2.8	31	85	7	102	40	15	10	33	1.82
29989344--29989426	31	2.7	31	83	7	91	27	12	7	53	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29990418--29990461	19	2.4	19	84	3	54	77	2	18	2	0.98
29994071--29994111	21	2.0	21	90	0	64	29	21	29	19	1.98
30005649--30005815	43	3.9	43	75	7	153	28	14	23	32	1.94
30011373--30011400	4	7.0	4	100	0	56	0	0	50	50	1.00
30011419--30011452	2	17.5	2	87	6	52	52	0	47	0	1.00
30016509--30016544	16	2.2	16	90	0	54	41	5	22	30	1.76
30016722--30016843	58	2.1	58	86	6	167	52	3	1	42	1.27
30018048--30018091	19	2.4	19	84	3	54	77	2	18	2	0.98
30032270--30032414	43	3.4	43	76	11	122	28	15	23	31	1.96
30038008--30038035	4	7.0	4	100	0	56	0	0	50	50	1.00
30038054--30038089	2	18.5	2	88	5	56	52	0	47	0	1.00
30042333--30042827	208	2.4	210	78	7	504	38	14	6	40	1.72
30043406--30043441	16	2.2	16	90	0	54	41	5	22	30	1.76
30043621--30043742	58	2.1	58	86	6	167	52	3	1	42	1.27
30044946--30044989	19	2.4	19	84	3	54	77	2	18	2	0.98
30048597--30048637	21	2.0	21	90	0	64	29	21	29	19	1.98
30052045--30052154	54	2.0	54	87	3	159	34	8	31	25	1.85
30060168--30060334	43	3.9	43	75	7	153	28	14	23	32	1.94
30065895--30065922	4	7.0	4	100	0	56	0	0	50	50	1.00
30065941--30065976	2	18.5	2	88	5	56	52	0	47	0	1.00
30070220--30070714	208	2.4	210	78	7	504	38	14	6	40	1.72
30071509--30071630	58	2.1	58	86	6	167	52	3	1	42	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30075726--30075762	19	1.9	19	88	0	56	43	2	16	37	1.62
30076345--30076372	12	2.3	12	100	0	56	39	0	0	60	0.97
30076475--30076511	17	2.1	18	90	5	58	72	0	27	0	0.84
30076868--30076901	17	1.9	18	88	5	52	41	0	23	35	1.55
30077374--30077413	13	2.9	14	85	7	55	62	0	10	27	1.27
30077776--30077837	21	2.9	22	88	9	92	17	25	25	30	1.97
30077776--30077850	21	3.5	21	83	5	89	17	22	24	36	1.95
30080626--30080767	17	8.7	16	69	19	64	53	2	2	41	1.27
30080626--30080733	31	3.4	30	78	13	119	54	3	2	38	1.33
30080719--30080774	6	9.5	6	94	3	96	51	1	0	46	1.11
30081186--30081292	52	2.1	50	89	3	160	49	5	3	41	1.44
30090771--30090814	19	2.3	19	84	7	54	63	0	4	31	1.14
30090874--30090928	25	2.2	24	81	15	67	69	1	5	23	1.19
30090875--30090926	24	2.1	25	82	10	63	69	1	5	23	1.20
30093716--30093758	21	2.0	22	86	13	63	55	4	0	39	1.20
30098694--30098729	16	2.2	16	90	9	56	50	5	2	41	1.40
30099962--30099996	14	2.5	14	90	0	52	62	11	5	20	1.48
30100304--30100343	18	2.2	18	100	0	80	10	30	27	32	1.89
30100604--30100655	23	2.3	23	86	6	70	48	7	0	44	1.31
30100759--30100796	17	2.2	18	85	4	51	57	2	0	39	1.12
30104298--30104358	30	2.1	29	84	9	79	31	1	4	62	1.26
30105443--30105502	26	2.3	26	82	2	66	3	20	6	70	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30118051--30118545	87	5.6	86	73	13	319	26	20	20	32	1.97
30118138--30118462	175	1.8	177	88	3	505	27	20	19	33	1.96
30118112--30118545	175	2.4	177	79	8	493	27	20	20	32	1.97
30129478--30129531	21	2.6	21	90	0	90	20	5	44	29	1.74
30130297--30130329	17	2.0	17	88	5	50	33	18	0	48	1.48
30130612--30130793	46	4.0	46	87	0	229	22	23	14	39	1.91
30133868--30134045	43	4.2	43	87	2	247	42	20	9	27	1.83
30133872--30134045	85	2.1	83	86	4	242	43	20	9	27	1.83
30135395--30135453	30	1.9	31	86	10	86	47	1	20	30	1.60
30135691--30135746	11	4.9	11	85	8	67	33	0	1	64	1.04
30137860--30138116	46	5.7	46	88	5	328	42	14	22	21	1.88
30137879--30138088	87	2.4	87	86	4	285	40	15	22	21	1.90
30137863--30138116	133	1.9	133	87	1	375	42	13	22	21	1.88
30139398--30139427	15	2.0	15	100	0	60	40	40	6	13	1.71
30139712--30139946	62	3.8	62	92	1	344	48	14	11	25	1.77
30139855--30139957	34	3.1	34	62	25	85	48	17	8	25	1.75
30139843--30140096	112	2.3	112	90	0	409	47	16	12	24	1.80
30139907--30140015	48	2.3	48	91	0	182	46	14	11	26	1.79
30139955--30140087	64	2.1	64	94	0	230	45	15	14	24	1.83
30139967--30140069	34	3.1	34	63	25	85	45	14	12	27	1.81
30140229--30140311	18	4.9	18	69	21	63	53	15	6	25	1.65
30140227--30140266	12	3.3	12	82	0	53	55	17	2	25	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30140328--30140376	12	4.1	12	82	10	55	57	12	8	22	1.61
30140328--30140370	18	2.4	18	80	0	50	55	11	9	23	1.64
30140905--30140977	31	2.4	29	78	17	85	21	9	20	47	1.78
30152821--30152860	3	13.3	3	100	0	80	0	32	0	67	0.91
30155608--30155645	19	2.0	20	89	5	60	42	10	23	23	1.85
30161542--30161625	26	3.2	26	94	0	141	36	23	4	34	1.76
30164785--30164818	12	2.9	12	86	4	52	32	0	0	67	0.91
30170001--30170058	8	7.0	8	79	12	64	67	0	3	29	1.07
30170001--30170056	3	19.0	3	75	17	55	66	0	3	30	1.09
30170001--30170058	18	3.5	17	86	9	75	67	0	3	29	1.07
30170014--30170074	18	3.5	17	75	20	56	67	0	4	27	1.11
30178811--30178868	26	2.2	26	93	0	98	34	5	24	36	1.78
30185754--30185794	19	2.1	20	86	4	57	9	29	14	46	1.77
30187236--30187349	33	3.5	32	78	9	104	31	12	25	30	1.92
30187263--30187351	33	2.7	33	81	8	110	32	10	25	31	1.89
30188050--30188098	18	2.5	20	87	6	66	59	8	2	30	1.38
30188220--30188265	3	15.7	3	78	13	51	65	0	4	30	1.12
30188220--30188265	21	2.2	20	85	7	65	65	0	4	30	1.12
30189900--30189956	22	2.7	19	78	10	51	49	5	0	45	1.24
30196052--30196081	15	1.9	16	93	6	53	80	0	13	6	0.91
30202723--30202787	31	2.1	31	82	2	78	49	1	0	49	1.10
30202736--30202775	21	1.9	21	84	0	53	47	0	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30202735--30202796	31	2.0	32	87	3	90	48	1	0	50	1.10
30213318--30213367	26	2.0	25	88	7	75	62	4	0	34	1.14
30213342--30213410	12	6.3	11	74	11	61	63	7	1	27	1.29
30221144--30221174	16	1.9	16	93	0	53	41	0	3	54	1.16
30221254--30221284	12	2.6	12	94	0	53	74	0	25	0	0.82
30223905--30224015	47	2.4	47	83	6	145	36	23	15	25	1.94
30224778--30224802	4	6.2	4	100	0	50	0	24	0	76	0.80
30226093--30226127	17	2.0	18	88	5	54	60	0	11	28	1.32
30228411--30228451	18	2.4	17	84	8	55	7	9	2	80	0.99
30228523--30228579	23	2.4	24	85	5	80	36	0	7	56	1.27

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