genome.fa.s12.2.7.7.80.10.50.1000.16.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: A12
Parameters: 2 7 7 80 10 50 1000
Length:  103038859

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   

This is table  16  of  320  ( 38372 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)
4394716--4394750	17	2.1	17	100	0	70	22	5	20	51	1.68
4397543--4397652	27	4.1	27	88	9	179	46	12	7	33	1.70
4397530--4397645	54	2.2	54	98	1	225	46	13	7	31	1.72
4401039--4401079	16	2.6	17	81	14	52	39	17	4	39	1.71
4401836--4401868	13	2.4	14	95	5	59	0	21	0	78	0.75
4402086--4402125	5	8.0	5	94	0	71	60	2	0	37	1.11
4402929--4402973	23	2.0	23	86	0	63	64	0	4	31	1.13
4404277--4404316	19	2.1	19	85	0	53	50	2	0	47	1.14
4405835--4405908	29	2.5	29	86	4	94	21	13	16	48	1.80
4406772--4406805	17	2.0	17	88	0	50	41	0	0	58	0.98
4411409--4411474	29	2.2	30	91	2	107	28	0	13	57	1.37
4411937--4411990	27	2.0	27	100	0	108	37	3	11	48	1.57
4412134--4412194	31	2.0	31	84	6	81	67	1	4	26	1.20
4412580--4412615	18	2.1	18	89	5	56	52	0	2	44	1.15
4414486--4414541	28	2.0	27	83	10	69	35	0	14	50	1.43
4414853--4414905	25	2.2	24	86	3	70	16	20	22	39	1.92
4417101--4417153	16	3.2	16	79	10	54	26	0	1	71	0.96
4417106--4417183	39	2.0	39	82	12	97	28	0	2	69	1.02
4425135--4425195	20	3.0	20	100	0	122	29	14	24	31	1.95
4445710--4445827	18	6.3	19	70	22	79	11	21	1	66	1.32
4445802--4445837	17	2.1	17	89	5	54	11	16	0	72	1.12
4452186--4452210	6	4.2	6	100	0	50	20	0	0	80	0.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4452269--4452296	13	2.2	13	100	0	56	53	0	7	39	1.28
4453932--4453995	13	4.9	13	96	0	119	39	28	9	23	1.86
4459740--4459791	24	2.2	24	89	0	77	55	9	1	32	1.43
4461709--4461760	24	2.2	24	89	0	77	55	9	1	32	1.43
4463295--4463326	5	6.6	5	92	7	57	18	0	0	81	0.70
4463295--4463325	9	3.3	9	91	8	53	19	0	0	80	0.71
4467747--4467778	5	6.6	5	92	7	57	18	0	0	81	0.70
4467747--4467777	9	3.3	9	91	8	53	19	0	0	80	0.71
4468695--4468835	40	3.6	38	75	12	108	31	21	17	29	1.96
4468993--4469039	24	2.0	24	84	16	62	51	17	0	31	1.46
4469710--4469787	36	2.2	36	81	9	97	39	6	2	51	1.41
4479340--4479381	21	2.0	21	85	4	57	57	0	0	42	0.99
4483276--4483303	2	14.0	2	100	0	56	50	50	0	0	1.00
4486951--4487008	30	1.9	29	86	6	80	41	13	10	34	1.79
4500479--4500565	44	2.0	44	100	0	174	20	31	9	39	1.84
4500662--4500701	15	2.6	15	88	4	53	27	20	12	40	1.88
4503940--4503996	28	2.0	28	93	0	96	24	1	14	59	1.44
4514223--4514622	69	5.8	68	80	2	363	33	22	23	21	1.97
4514223--4514618	207	1.9	207	82	3	492	33	22	22	21	1.97
4520525--4520551	7	3.9	7	100	0	54	88	0	0	11	0.50
4520628--4520666	13	2.8	14	84	7	53	51	0	0	48	1.00
4520688--4520728	21	2.0	21	95	0	73	78	4	14	2	1.03
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4530747--4530799	11	4.6	11	80	15	63	75	0	5	18	0.99
4530751--4530796	24	1.9	24	86	8	67	73	0	6	19	1.04
4530741--4530799	11	5.3	11	78	9	57	76	0	5	18	0.97
4538402--4538450	24	2.1	23	81	11	55	24	14	14	46	1.81
4549733--4549762	13	2.2	14	94	5	53	26	0	0	73	0.84
4555499--4555523	12	2.1	12	100	0	50	24	8	24	44	1.80
4558868--4559304	122	3.5	126	85	4	562	28	15	15	40	1.87
4559393--4559596	34	6.7	28	71	23	114	43	16	0	39	1.52
4559444--4559547	54	2.0	54	87	11	153	42	13	0	44	1.44
4559529--4559611	34	2.4	35	84	9	100	46	12	0	40	1.41
4561000--4561120	57	2.1	57	100	0	242	38	17	18	25	1.92
4570661--4570697	20	1.9	20	88	5	58	40	0	8	51	1.32
4572849--4573169	46	7.0	46	90	0	426	39	15	24	21	1.91
4575706--4575753	24	2.0	25	91	4	80	64	4	12	18	1.43
4578085--4578299	53	4.2	53	81	6	216	27	15	25	31	1.96
4579140--4579213	37	2.0	37	89	0	112	16	27	31	25	1.96
4579787--4579841	22	2.5	22	88	2	85	16	27	0	56	1.40
4590399--4590438	16	2.6	14	82	17	53	2	25	0	72	0.97
4591407--4591449	21	2.0	21	86	8	61	20	9	11	58	1.61
4592692--4592733	9	4.0	10	82	17	50	23	0	0	76	0.79
4594211--4594337	42	3.0	42	86	6	170	29	26	14	29	1.95
4594296--4594417	47	2.6	46	86	1	163	29	27	15	27	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4594451--4594591	31	4.5	31	91	0	219	25	26	19	28	1.98
4594573--4594695	50	2.4	51	90	5	196	26	22	15	35	1.94
4594811--4594839	14	2.0	15	93	6	51	55	17	6	20	1.65
4605089--4605395	41	7.5	41	86	2	386	33	21	22	22	1.97
4605089--4605396	123	2.5	122	87	3	431	34	21	22	22	1.97
4605558--4605635	21	3.6	21	69	19	61	30	1	23	44	1.61
4605920--4605965	21	2.2	21	84	0	56	21	2	32	43	1.65
4611489--4611544	9	5.9	9	76	12	58	46	21	1	30	1.62
4617090--4617137	21	2.3	21	92	0	78	25	14	58	2	1.48
4617430--4617612	43	4.3	43	79	5	158	27	19	21	31	1.97
4627881--4627916	18	1.9	19	88	5	56	22	0	2	75	0.94
4632961--4633029	21	3.4	21	71	15	72	36	1	7	55	1.37
4633016--4633046	15	2.1	14	94	5	53	35	3	6	54	1.42
4643800--4643864	18	3.6	19	71	23	59	72	1	0	26	0.94
4643800--4643867	15	4.4	16	75	17	72	72	1	0	26	0.94
4643800--4643867	30	2.3	30	81	18	90	72	1	0	26	0.94
4644471--4644515	13	3.6	13	77	20	51	24	0	4	71	1.05
4644464--4644514	24	2.1	24	86	13	70	25	0	1	72	0.95
4647273--4647338	31	2.1	31	88	0	96	24	24	31	19	1.98
4650652--4650685	15	2.2	16	90	10	54	26	0	0	73	0.83
4653463--4653522	31	1.9	31	86	3	84	48	5	0	46	1.24
4655236--4655277	3	13.7	3	85	5	57	69	0	0	30	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4655236--4655276	12	3.3	12	93	3	64	70	0	0	29	0.87
4655787--4655833	12	3.5	13	78	13	51	63	2	0	34	1.06
4659630--4659671	22	1.9	22	90	0	66	33	9	11	45	1.73
4667896--4667946	21	2.4	21	86	0	66	33	31	5	29	1.81
4668874--4669245	63	5.9	63	81	2	372	24	25	21	28	1.99
4668884--4669256	126	3.0	126	83	1	417	25	26	20	27	1.99
4677316--4677371	25	2.2	25	96	0	103	35	19	17	26	1.94
4680231--4682642	804	3.0	804	98	0	4628	31	18	24	25	1.98
4686210--4686719	44	11.6	44	69	8	270	34	20	22	21	1.97
4686305--4686587	87	3.2	87	79	4	311	35	21	21	21	1.96
4686209--4686499	131	2.2	131	93	0	492	34	21	21	22	1.97
4686209--4686543	131	2.6	131	87	2	397	34	21	22	21	1.97
4686567--4686762	87	2.2	87	81	5	225	35	19	25	19	1.96
4686392--4686763	44	8.5	43	67	14	125	34	20	24	20	1.96
4687121--4687194	38	1.9	38	100	0	148	41	33	2	21	1.67
4690298--4690344	12	4.1	12	78	8	53	29	10	0	59	1.31
4690392--4690440	12	3.8	12	80	15	53	32	8	4	55	1.48
4694042--4694139	38	2.5	38	83	9	110	25	22	23	28	1.99
4694078--4694161	38	2.2	38	91	0	132	23	21	22	32	1.98
4695743--4695920	43	4.2	43	91	1	286	11	24	33	30	1.91
4696074--4696242	58	2.9	58	91	0	277	23	18	28	28	1.98
4696077--4696178	29	3.5	29	70	10	91	23	20	26	29	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4696106--4696208	29	3.6	29	71	10	93	23	16	31	29	1.96
4699803--4699903	38	2.6	38	84	9	116	24	22	24	27	2.00
4699839--4699922	38	2.2	38	93	0	141	22	21	23	32	1.98
4702155--4702193	13	3.0	13	88	7	53	35	0	0	64	0.94
4703184--4703302	59	2.0	59	98	0	229	41	9	5	44	1.58
4705568--4705597	15	2.1	14	93	6	51	13	0	43	43	1.43
4715060--4715093	3	11.7	3	87	6	52	2	29	0	67	1.05
4718189--4718251	28	2.2	28	77	11	65	42	0	1	55	1.09
4718519--4718563	15	2.9	16	80	6	56	31	4	2	62	1.27
4728753--4728783	11	2.8	11	95	0	53	19	25	35	19	1.95

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