genome.fa.s2.2.7.7.80.10.50.1000.134.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  134  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)
43868207--43868278	35	2.0	37	91	8	121	37	11	15	36	1.83
43868209--43868285	17	4.4	16	78	13	64	36	11	16	35	1.86
43868270--43868314	23	2.0	23	83	8	58	33	6	15	44	1.73
43872814--43872851	19	2.0	20	84	5	51	26	23	0	50	1.50
43872938--43872981	18	2.6	17	83	16	56	31	29	0	38	1.58
43877398--43877439	13	3.2	13	83	9	59	73	0	26	0	0.83
43880060--43880095	18	2.1	17	89	5	54	50	0	5	44	1.25
43888939--43888975	17	2.2	17	95	0	65	54	5	8	32	1.53
43897808--43897992	79	2.3	81	83	7	227	24	27	22	24	2.00
43897808--43897992	40	4.7	40	82	7	225	24	27	22	24	2.00
43901091--43901161	13	5.5	13	84	0	79	38	26	7	28	1.82
43901091--43901159	26	2.6	27	79	6	88	37	26	7	28	1.83
43901085--43901161	39	2.0	39	86	0	109	35	27	6	31	1.82
43908324--43908386	6	10.5	6	92	0	99	79	3	1	15	0.94
43910675--43911063	198	2.0	196	84	2	510	21	26	22	29	1.99
43920603--43920638	17	2.1	17	100	0	72	30	0	5	63	1.17
43920597--43920662	28	2.4	29	76	16	70	30	1	6	62	1.29
43920680--43920710	14	2.2	14	94	0	53	12	0	3	83	0.75
43922349--43922406	30	1.9	30	85	0	80	29	25	17	27	1.97
43924659--43924705	24	2.0	24	82	0	58	38	14	19	27	1.91
43925227--43925277	23	2.2	23	92	0	84	15	39	27	17	1.90
43926835--43926902	35	1.9	35	93	0	118	27	35	23	13	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43926876--43926929	28	1.9	28	88	0	81	40	31	16	11	1.84
43927655--43927694	13	3.0	13	85	7	53	10	10	0	80	0.92
43927671--43927736	9	6.4	9	74	19	51	4	9	4	81	0.96
43927688--43927735	20	2.4	19	80	13	51	6	8	6	79	1.07
43928426--43928927	250	2.0	252	96	0	927	28	17	20	33	1.96
43935384--43935454	35	2.0	35	97	0	133	28	33	23	14	1.94
43937218--43937275	24	2.5	23	81	16	66	62	0	5	32	1.18
43939553--43939623	30	2.3	31	85	11	92	50	0	2	46	1.16
43941701--43941905	62	3.3	62	79	6	184	21	25	26	26	1.99
43941752--43941913	62	2.6	62	85	0	216	22	25	25	25	2.00
43947368--43947408	16	2.5	16	84	4	55	78	4	9	7	1.10
43948438--43948465	12	2.3	12	100	0	56	25	46	17	10	1.80
43948980--43949009	3	10.0	3	92	0	51	63	0	3	33	1.11
43965933--43966077	19	7.9	19	87	9	230	35	12	15	36	1.85
43965939--43966077	54	2.6	54	100	0	278	35	12	15	36	1.85
43965941--43966077	35	3.8	36	85	10	199	35	13	14	36	1.85
43965932--43966084	73	2.1	71	88	8	229	36	11	15	35	1.84
43965933--43966100	19	8.8	22	85	10	102	35	11	15	37	1.83
43966368--43966403	18	2.1	17	89	5	54	33	0	0	66	0.92
43977916--43977975	30	2.0	30	90	6	95	38	6	26	28	1.81
43981468--43981506	15	2.5	15	91	4	60	15	12	15	56	1.68
43985860--43986326	220	2.1	220	91	0	745	32	18	21	27	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43987668--43987703	17	2.2	16	90	5	54	61	5	2	30	1.33
43987926--43988001	18	4.4	17	72	11	57	65	1	7	25	1.27
43989495--43989530	17	2.2	16	90	5	54	61	5	2	30	1.33
43989757--43989832	18	4.4	17	72	11	57	65	1	7	25	1.27
43991024--43991708	78	8.8	78	90	1	883	33	17	23	25	1.96
43991024--43991708	234	2.9	234	86	3	973	33	17	23	25	1.96
43991737--43991904	45	3.8	45	86	1	230	30	13	28	27	1.94
43991738--43991907	89	1.9	89	88	0	259	30	13	28	27	1.94
43991722--43991915	45	4.3	45	84	1	228	32	13	27	26	1.94
43992304--43992350	18	2.5	19	96	3	87	36	12	14	36	1.85
43992642--43992675	18	1.9	17	88	5	50	29	0	0	70	0.87
43994122--43994276	66	2.3	65	79	8	161	32	25	10	30	1.89
44018871--44018961	19	4.9	19	90	8	152	38	10	14	36	1.81
44018879--44018968	35	2.5	37	89	10	143	38	11	14	35	1.82
44019604--44019637	18	1.9	17	94	5	59	38	8	0	52	1.33
44024280--44024347	12	6.0	11	71	19	50	82	0	14	2	0.79
44024281--44024347	23	3.0	21	83	10	80	82	0	14	2	0.79
44024297--44024345	15	3.2	16	80	8	66	83	0	14	2	0.73
44024282--44024347	7	9.1	7	75	18	64	81	0	15	3	0.80
44024300--44024347	16	3.1	16	82	11	64	81	0	16	2	0.79
44025307--44025577	84	3.2	84	80	7	323	30	20	23	24	1.98
44025583--44026377	207	3.8	207	94	0	1293	29	17	23	30	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44026766--44026856	19	4.9	19	85	8	134	37	9	16	36	1.82
44026774--44026863	35	2.5	37	85	10	125	37	10	16	35	1.82
44031153--44031228	10	7.5	10	69	18	50	39	10	2	47	1.52
44037665--44037693	5	5.8	5	100	0	58	17	0	0	82	0.66
44039190--44039265	22	3.7	21	76	15	68	40	17	6	35	1.75
44039226--44039316	19	4.9	19	90	8	152	35	15	12	37	1.84
44039219--44039316	35	2.7	37	86	12	141	34	16	11	37	1.84
44039240--44039295	17	3.5	15	88	9	60	35	16	10	37	1.83
44039435--44039475	21	2.0	21	85	0	55	9	2	14	73	1.19
44039674--44039823	45	3.3	45	89	0	219	24	28	15	32	1.95
44039816--44039958	47	3.2	47	63	15	129	27	23	20	28	1.99
44039770--44040001	88	2.6	88	93	2	383	26	25	18	28	1.98
44040135--44040506	78	4.8	78	86	1	503	25	23	18	32	1.97
44039881--44040270	209	1.9	209	86	2	559	26	23	18	30	1.98
44043274--44043476	100	2.0	100	98	0	388	30	25	17	27	1.97
44058664--44058769	36	3.1	36	75	18	118	32	30	12	25	1.92
44058700--44058758	30	2.0	30	93	0	100	32	28	13	25	1.94
44066169--44066338	85	2.0	85	98	0	331	18	26	24	30	1.98
44066813--44066926	47	2.5	44	76	17	115	36	6	0	57	1.24
44067195--44067260	17	3.9	17	73	16	66	34	1	0	63	1.04
44073703--44073735	5	6.6	5	100	0	66	18	0	0	81	0.68
44077940--44077967	5	5.6	5	100	0	56	17	0	0	82	0.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44085894--44086013	56	2.1	56	98	0	231	45	9	21	23	1.80
44087182--44087325	40	3.6	40	79	12	145	25	23	27	24	2.00
44087234--44087332	39	2.5	39	86	4	110	25	22	28	24	1.99
44087181--44087331	79	1.9	80	81	6	182	25	23	27	23	2.00
44090559--44090634	10	7.5	10	69	18	50	39	10	2	47	1.52
44096626--44097216	294	2.0	294	100	0	1182	37	16	17	27	1.92
44097227--44097302	22	3.7	21	76	15	68	40	17	6	35	1.75
44097256--44097353	35	2.7	37	87	12	150	35	16	10	37	1.82
44097263--44097353	19	4.9	19	92	8	161	36	15	10	37	1.83
44097703--44097976	45	6.1	45	78	8	261	26	25	15	32	1.96
44097703--44097902	89	2.2	90	86	1	276	25	27	15	33	1.95
44097916--44098210	78	3.8	78	92	0	448	26	22	17	32	1.96
44098282--44098651	78	4.8	78	88	2	510	25	23	18	32	1.97
44098282--44098651	155	2.4	156	87	1	528	25	23	18	32	1.97
44109759--44109936	27	6.6	27	84	3	205	29	28	15	26	1.96
44109780--44109935	82	1.9	81	88	3	233	29	28	15	26	1.96
44117824--44118001	27	6.6	27	84	3	205	29	28	15	26	1.96
44117845--44118000	82	1.9	81	88	3	233	29	28	15	26	1.96
44120948--44121361	207	2.0	207	98	0	792	39	17	13	29	1.88
44122699--44122741	22	1.9	22	85	4	59	39	16	6	37	1.75
44122720--44122810	19	4.9	19	89	8	143	34	15	13	37	1.86
44122713--44122810	35	2.7	37	83	12	132	33	16	12	37	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44124280--44124341	18	3.4	18	78	14	65	58	0	6	35	1.24
44124743--44124792	16	3.0	17	82	5	57	28	2	2	68	1.12
44126118--44126334	46	4.7	46	97	0	407	26	28	25	19	1.99
44128372--44128526	66	2.3	66	78	2	159	31	23	14	30	1.94
44132956--44133017	31	2.0	31	90	0	97	46	22	6	24	1.75
44140209--44140304	30	2.9	35	71	19	87	31	30	10	28	1.90
44146734--44146804	36	2.0	36	97	0	133	35	21	11	32	1.89
44161358--44161394	18	2.1	18	100	0	74	40	10	0	48	1.38
44162818--44162862	19	2.3	19	84	3	54	37	6	2	53	1.40
44167390--44167497	26	4.2	26	93	0	189	36	24	7	32	1.83

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