genome.fa.s8.2.7.7.80.10.50.1000.164.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_chr9
Parameters: 2 7 7 80 10 50 1000
Length:  91122320

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   

This is table  164  of  279  ( 33431 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)
54183667--54183706	21	1.9	21	90	10	64	17	0	15	67	1.23
54187552--54187597	12	3.6	12	78	16	56	65	0	0	34	0.93
54187552--54187614	27	2.4	26	79	10	74	60	0	3	36	1.13
54188814--54188839	12	2.2	12	100	0	52	57	0	0	42	0.98
54212136--54212250	60	1.9	60	87	5	171	43	6	5	45	1.51
54216710--54216770	31	2.0	31	93	0	104	54	6	1	37	1.37
54228032--54228072	11	3.7	11	100	0	82	17	7	0	75	1.02
54228587--54228647	32	1.9	32	89	0	95	40	9	1	47	1.46
54234746--54234860	44	2.6	44	85	2	149	35	13	22	27	1.92
54234746--54234879	46	3.0	45	82	4	153	35	14	23	26	1.93
54237189--54237247	28	2.0	30	84	12	79	54	3	1	40	1.27
54253448--54253488	21	2.0	21	90	0	64	29	21	29	19	1.98
54257862--54257935	35	2.2	35	88	9	109	35	9	6	48	1.62
54258007--54258036	14	2.1	14	93	0	51	46	10	0	43	1.37
54277245--54277273	12	2.3	13	94	5	51	68	0	27	3	1.05
54282379--54282420	21	2.0	21	100	0	84	52	23	14	9	1.71
54292735--54292787	20	2.7	21	83	13	69	62	0	3	33	1.13
54292735--54292799	20	3.3	20	79	14	64	60	0	6	33	1.22
54311017--54311060	22	2.0	22	90	0	70	38	6	6	47	1.57
54315855--54315909	22	2.7	20	84	13	76	36	0	0	63	0.95
54315835--54315900	24	2.8	24	81	4	73	36	0	0	63	0.95
54324299--54324357	24	2.5	23	83	8	73	66	0	0	33	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54326215--54326291	25	3.0	26	74	16	72	62	6	5	25	1.41
54326684--54326722	17	2.4	16	83	8	51	64	10	2	23	1.37
54326743--54326767	5	5.0	5	100	0	50	80	0	0	20	0.72
54327606--54327658	25	2.1	25	82	0	61	26	16	5	50	1.67
54334615--54334651	19	1.9	19	88	0	56	27	2	2	67	1.17
54338407--54338432	13	2.0	13	100	0	52	38	0	0	61	0.96
54338890--54338989	49	2.1	47	81	10	114	63	1	4	32	1.20
54341341--54341373	14	2.4	14	85	15	50	72	15	12	0	1.12
54345196--54345221	13	2.0	13	100	0	52	7	0	15	76	0.99
54345243--54345271	6	4.8	6	100	0	58	65	0	0	34	0.93
54345993--54346052	31	2.0	31	81	12	72	53	1	1	43	1.20
54348138--54348180	19	2.3	19	80	8	52	51	4	2	41	1.35
54348543--54348600	29	2.0	30	86	3	82	37	1	8	51	1.43
54348703--54348742	20	2.0	20	100	0	80	50	0	0	50	1.00
54352090--54352181	46	2.0	46	97	0	175	36	13	22	27	1.91
54354424--54354832	38	9.9	38	92	6	512	34	16	25	22	1.95
54354614--54354876	46	5.7	46	93	0	402	38	15	24	21	1.92
54354538--54354876	138	2.6	129	86	8	433	37	15	24	22	1.93
54356576--54356614	12	3.2	12	81	0	51	25	38	7	28	1.83
54357216--54357291	27	2.8	26	88	7	91	35	0	1	63	1.03
54357236--54357275	20	2.0	20	85	9	55	37	0	0	62	0.95
54357240--54357300	27	2.3	27	91	0	95	37	1	1	59	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54358423--54358462	21	2.0	21	85	5	55	77	2	15	5	1.04
54372659--54372699	15	2.6	16	88	7	57	46	0	2	51	1.14
54390620--54390660	7	6.1	7	82	5	50	51	2	0	46	1.14
54391660--54391702	11	3.8	11	80	17	52	30	2	2	65	1.18
54398628--54398665	20	1.9	20	88	0	58	26	0	5	68	1.11
54407274--54407321	24	2.0	24	100	0	96	58	12	16	12	1.63
54407577--54407624	25	1.9	25	87	8	71	31	8	22	37	1.84
54421496--54421561	33	2.0	33	100	0	132	45	12	15	27	1.81
54437008--54437097	33	2.5	38	74	20	93	42	1	3	53	1.24
54440314--54440376	20	3.0	21	77	15	67	69	3	4	22	1.21
54441224--54441318	21	4.5	22	66	22	69	55	5	6	32	1.47
54441209--54441337	63	2.0	64	95	3	233	55	4	6	32	1.47
54450592--54450642	25	2.0	25	96	0	93	31	11	11	45	1.77
54451155--54451185	11	2.8	11	95	0	53	51	0	0	48	1.00
54451349--54451383	18	1.9	18	88	0	52	57	5	5	31	1.46
54457041--54457215	47	3.6	48	83	6	194	24	18	28	29	1.98
54464397--54464424	3	9.3	3	100	0	56	35	32	0	32	1.58
54476541--54476580	15	2.6	15	88	4	53	32	0	0	67	0.91
54476928--54476953	11	2.4	11	100	0	52	92	0	0	7	0.39
54482401--54482453	15	3.6	14	78	16	54	26	0	3	69	1.05
54487405--54487522	2	59.0	2	100	0	236	0	50	0	50	1.00
54498714--54498772	23	2.6	23	100	0	118	32	13	18	35	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54506805--54506830	12	2.2	12	100	0	52	34	7	34	23	1.83
54508201--54508245	16	2.9	16	78	18	51	42	4	0	53	1.21
54510688--54510744	21	2.8	21	89	5	82	31	7	5	56	1.49
54513580--54513667	30	2.9	30	88	6	117	35	37	15	11	1.84
54513733--54513775	18	2.4	18	88	0	59	18	27	6	46	1.75
54517039--54517077	19	2.1	19	95	0	69	51	10	5	33	1.58
54517923--54517972	15	3.3	15	82	0	73	36	2	12	50	1.51
54518609--54518649	19	2.2	19	87	12	59	46	0	24	29	1.53
54518597--54518636	13	3.2	13	80	19	50	50	0	25	25	1.50
54521020--54521391	126	3.0	126	96	0	681	24	20	19	35	1.96
54521513--54521585	19	3.8	19	75	7	58	43	20	4	31	1.70
54521649--54521700	21	2.5	21	90	0	77	48	30	1	19	1.60
54522429--54522458	6	5.0	6	91	0	51	53	0	16	30	1.44
54523501--54523532	6	5.3	6	96	0	55	0	31	15	53	1.43
54523943--54523970	14	2.0	14	100	0	56	42	14	0	42	1.45
54524886--54524926	21	2.0	21	90	0	64	41	14	7	36	1.74
54534999--54535034	4	9.0	4	93	0	63	47	0	2	50	1.15
54535164--54535228	28	2.3	28	89	0	94	53	13	13	18	1.72
54535176--54535296	28	4.2	29	77	19	137	51	9	18	20	1.74
54535212--54535306	32	3.2	32	73	26	116	44	9	21	25	1.82
54535193--54535306	59	1.9	60	96	3	214	46	10	19	23	1.81
54535706--54535770	19	3.0	20	76	24	69	63	29	3	4	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54535685--54535737	27	2.0	27	96	0	97	73	18	3	3	1.14
54535705--54535780	25	3.3	24	79	17	81	64	27	2	5	1.28
54535727--54535780	24	2.2	24	90	6	83	62	29	1	5	1.28
54535677--54535780	44	2.3	45	77	8	113	60	30	2	5	1.35
54536200--54536249	22	2.3	22	82	0	55	0	42	0	58	0.98
54538636--54538743	25	4.3	25	91	2	164	25	26	15	31	1.96
54538736--54538785	22	2.2	24	82	13	61	16	32	14	38	1.88
54539579--54539630	23	2.2	24	82	3	61	48	1	1	48	1.24
54539765--54539795	16	1.9	16	93	0	53	41	0	3	54	1.16
54545097--54545123	13	2.1	13	100	0	54	29	14	29	25	1.95
54545499--54545552	26	2.1	26	100	0	108	44	14	14	25	1.84
54545870--54546399	292	1.8	292	100	0	1060	35	6	18	39	1.77
54549685--54549727	15	2.9	14	80	13	50	60	2	0	37	1.10
54556796--54556845	21	2.4	21	89	0	73	36	34	4	26	1.75
54557143--54557174	11	3.1	11	82	17	50	68	0	0	31	0.90
54557136--54557174	20	2.0	20	94	0	69	69	0	0	30	0.89
54557136--54557178	9	4.7	9	81	16	52	72	0	0	27	0.85
54562359--54562393	16	2.4	14	90	9	52	34	0	2	62	1.10
54575281--54575321	20	2.0	20	85	9	55	21	0	2	75	0.92
54575417--54575471	27	2.0	27	92	0	92	12	9	9	69	1.38
54584854--54584946	18	5.2	18	90	0	150	27	24	16	31	1.96
54590194--54590243	25	2.0	25	100	0	100	32	8	4	56	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54593166--54593197	2	16.0	2	93	0	55	53	0	46	0	1.00
54594632--54594684	21	2.5	21	90	0	79	30	39	11	18	1.86
54610276--54610319	19	2.3	19	88	7	63	56	0	4	38	1.20
54627363--54627635	135	2.0	134	95	0	492	37	17	13	31	1.89
54636218--54636260	21	2.0	21	100	0	86	30	13	9	46	1.75
54639687--54639768	19	4.3	19	71	11	69	60	1	2	35	1.17
54639692--54639806	57	2.0	58	84	6	153	61	1	5	31	1.28
54639688--54639826	57	2.5	52	74	15	125	60	1	5	33	1.27
54639677--54639828	10	15.6	10	66	15	61	61	1	4	32	1.24
54640389--54640433	19	2.3	21	85	11	60	57	4	2	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