genome.fa.s5.2.7.7.80.10.50.1000.11.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  11  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)
3924358--3924408	5	10.4	5	95	4	95	41	0	0	58	0.98
3924892--3924950	21	2.7	23	80	15	81	13	23	27	35	1.92
3924899--3924962	21	3.0	21	83	0	74	12	21	26	39	1.89
3925500--3925577	2	43.5	2	68	29	52	44	0	3	51	1.19
3925500--3925574	13	5.9	13	70	27	63	44	0	4	52	1.20
3925542--3925576	5	7.0	5	90	9	54	42	0	0	57	0.99
3925850--3925876	13	2.1	13	100	0	54	29	0	7	62	1.22
3925976--3926217	50	4.7	50	86	4	297	26	24	29	19	1.99
3925976--3926225	100	2.4	103	88	6	364	26	24	29	20	1.99
3928144--3928179	5	7.4	5	93	6	65	41	0	0	58	0.98
3928663--3928721	21	2.7	23	80	15	81	13	23	27	35	1.92
3957043--3957068	12	2.2	12	100	0	52	23	7	26	42	1.81
3965242--3965270	4	7.2	4	100	0	58	24	0	0	75	0.80
3970246--3970303	29	2.0	29	100	0	116	27	13	17	41	1.87
3971896--3971935	21	1.9	21	84	0	53	17	70	7	5	1.30
3977029--3977076	11	4.5	11	86	5	71	18	45	6	29	1.74
3977614--3977702	18	4.9	18	90	0	133	26	22	16	33	1.96
3978544--3978572	11	2.6	11	100	0	58	24	17	37	20	1.93
3983900--3984023	39	3.2	39	96	0	230	37	21	25	15	1.92
3983900--3984005	21	5.3	21	71	13	98	38	20	24	16	1.92
3983923--3984023	18	5.3	18	70	13	85	37	21	25	14	1.92
3985445--3985477	16	2.1	16	100	0	66	21	24	0	54	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3990187--3990212	2	13.0	2	100	0	52	50	0	50	0	1.00
3995698--3995739	18	2.2	20	83	8	52	52	7	9	30	1.61
4001193--4001248	23	2.4	23	100	0	112	14	25	32	28	1.94
4002185--4002228	18	2.5	17	85	3	61	63	0	0	36	0.95
4015504--4015588	42	2.0	42	95	0	152	32	7	20	40	1.79
4017830--4017901	31	2.2	33	83	9	87	56	11	2	29	1.48
4017848--4017916	33	2.2	31	84	10	86	56	10	4	28	1.51
4017981--4018025	23	2.0	23	86	0	63	35	2	15	46	1.58
4024570--4024597	14	2.0	14	100	0	56	28	0	21	50	1.49
4031552--4031603	19	2.7	19	82	14	54	55	3	1	38	1.29
4031742--4031781	12	3.2	12	82	6	53	40	0	2	57	1.12
4032238--4032281	20	2.2	20	80	11	56	43	0	6	50	1.29
4032720--4032761	21	2.0	22	85	4	59	57	0	7	35	1.26
4035166--4035196	3	10.0	3	93	6	53	0	35	0	64	0.94
4036383--4036409	6	4.5	6	100	0	54	18	14	33	33	1.92
4044691--4044730	17	2.4	17	83	4	55	20	0	2	77	0.88
4065806--4065846	21	1.9	22	85	5	57	53	4	2	39	1.35
4065884--4065957	21	3.6	22	75	15	68	63	2	8	25	1.35
4087967--4088032	31	2.1	31	82	0	78	30	3	12	54	1.52
4108462--4108507	22	2.1	22	91	0	74	39	4	8	47	1.54
4120637--4120735	23	4.3	23	89	0	144	24	21	25	29	1.99
4124515--4124545	12	2.6	12	94	0	53	0	25	0	74	0.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4124625--4124655	16	1.9	16	93	0	53	54	3	0	41	1.16
4126529--4126566	18	2.1	19	90	5	60	34	23	0	42	1.55
4127448--4127509	24	2.6	24	80	10	81	16	24	22	37	1.94
4127423--4127527	48	2.1	49	78	3	113	20	24	20	33	1.97
4130002--4130328	50	6.5	50	94	0	546	35	15	22	26	1.94
4130308--4130366	31	1.9	31	100	0	118	28	20	25	25	1.99
4130321--4130412	46	2.0	46	89	0	139	26	22	23	27	2.00
4130368--4130436	31	2.2	31	84	0	84	26	20	26	27	1.99
4135243--4135518	50	5.5	50	92	0	444	35	15	22	26	1.94
4135498--4135557	31	1.9	32	93	3	104	31	18	23	26	1.97
4142663--4142917	55	4.8	53	80	7	236	22	24	16	36	1.94
4142710--4142910	108	1.8	110	89	4	318	23	24	16	34	1.95
4145753--4145821	29	2.3	31	82	7	88	49	2	17	30	1.61
4145753--4145820	30	2.3	30	84	5	84	50	2	17	29	1.61
4147964--4148191	46	5.0	46	91	1	323	40	13	23	22	1.89
4148477--4148509	17	2.0	17	94	5	59	48	0	15	36	1.45
4150603--4150728	63	2.0	63	100	0	252	50	4	20	23	1.67
4150986--4151052	29	2.2	31	78	7	75	46	5	20	26	1.74
4156028--4156111	28	3.0	28	91	1	132	19	3	30	46	1.66
4156032--4156125	28	3.6	24	78	18	91	15	4	34	45	1.66
4156316--4156360	22	2.0	23	95	4	83	17	17	22	42	1.89
4157050--4157134	42	2.0	42	97	0	161	25	8	23	42	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4160861--4161133	46	5.9	46	90	1	388	41	13	23	21	1.88
4165455--4165533	4	19.2	4	69	10	52	5	25	5	64	1.35
4165558--4165588	14	2.2	14	94	0	53	22	16	0	61	1.34
4166201--4166233	17	2.0	17	94	5	59	48	0	15	36	1.45
4166803--4167120	165	1.9	167	95	1	577	37	2	9	50	1.48
4180632--4180669	17	2.1	19	85	9	53	52	7	0	39	1.31
4180692--4180770	40	2.0	41	85	7	108	60	3	3	31	1.32
4184701--4184729	3	9.7	3	100	0	58	34	0	0	65	0.93
4188294--4188554	129	2.0	129	100	0	522	40	16	16	27	1.89
4191059--4191088	15	2.0	15	93	0	51	76	0	3	20	0.92
4191363--4191494	64	2.0	66	91	5	216	41	16	15	26	1.88
4193071--4193185	46	2.5	46	88	0	176	37	12	6	43	1.69
4196753--4196797	16	2.8	16	82	0	63	60	13	0	26	1.34
4200924--4200961	20	1.9	20	88	0	58	42	7	5	44	1.56
4206966--4207004	14	2.8	14	88	0	51	48	10	2	38	1.51
4207700--4207763	32	2.0	32	100	0	128	40	25	3	31	1.71
4207881--4207932	25	2.1	25	85	0	68	59	5	3	30	1.39
4209136--4209181	15	3.1	15	70	17	51	21	8	13	56	1.63
4220042--4220087	16	3.1	14	79	14	56	71	2	0	26	0.97
4220033--4220102	11	6.5	11	75	15	58	67	2	1	28	1.14
4223709--4223795	21	4.0	23	79	10	92	37	25	20	16	1.93
4233603--4233648	24	2.0	23	82	4	56	41	10	19	28	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4239030--4239205	46	3.8	46	79	12	216	20	20	28	30	1.98
4239027--4239198	93	1.8	93	96	0	317	20	20	29	29	1.98
4240933--4241040	44	2.4	44	86	6	137	28	23	14	33	1.94
4248307--4248408	44	2.3	45	84	5	127	30	21	13	34	1.92
4254059--4254092	17	2.0	17	94	0	59	44	50	0	5	1.26
4258698--4258731	17	2.0	17	94	0	59	44	50	0	5	1.26
4259294--4259391	48	2.0	48	98	0	187	47	9	5	37	1.57
4259707--4259751	21	2.1	21	83	0	54	33	6	4	55	1.46
4270604--4270829	81	2.7	84	78	11	227	47	10	4	38	1.58
4286198--4286387	47	3.9	46	82	6	173	30	27	16	25	1.97
4291946--4291972	13	2.1	13	100	0	54	40	14	14	29	1.86
4301053--4301136	44	1.9	44	100	0	168	21	16	19	42	1.89
4305356--4305391	16	2.2	17	95	5	65	36	0	0	63	0.94
4306994--4307026	16	2.1	16	88	11	50	6	6	6	81	0.97
4314074--4314134	30	2.0	30	100	0	122	42	26	3	27	1.71
4319937--4319977	18	2.3	18	95	4	75	48	0	0	51	1.00
4320119--4320146	3	9.3	3	100	0	56	32	0	0	67	0.91
4325508--4325540	13	2.8	12	90	9	50	42	3	15	39	1.62
4329408--4329557	46	3.1	46	75	14	158	30	28	16	25	1.96
4330640--4330746	21	5.0	22	82	7	114	38	26	21	14	1.91
4330951--4331054	29	3.7	29	93	1	167	47	30	2	19	1.64
4330951--4331062	57	2.0	56	87	8	165	47	29	4	18	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4336716--4336863	46	3.2	47	91	1	203	22	23	15	38	1.92
4336842--4336883	20	2.1	20	100	0	84	26	26	14	33	1.94
4336796--4336929	66	2.0	66	97	0	250	23	25	15	35	1.94
4336862--4337009	46	3.2	46	98	0	278	23	25	14	35	1.93
4336721--4337009	158	1.8	158	93	1	499	22	24	15	37	1.93
4336765--4336975	112	1.9	112	96	0	395	23	25	16	35	1.94
4339411--4339478	30	2.3	30	84	5	84	27	19	5	47	1.72
4342174--4342442	46	5.8	46	95	0	441	22	24	15	37	1.92
4344546--4344680	39	3.4	39	72	15	109	28	27	20	23	1.99
4346551--4346631	44	1.9	41	83	16	103	55	8	0	35	1.31

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