genome.fa.s9.2.7.7.80.10.50.1000.118.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: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  70713020

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   

This is table  118  of  226  ( 27023 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)
40194456--40194664	83	2.5	82	91	0	337	28	23	23	23	1.99
40194704--40194825	40	3.1	38	78	9	129	21	19	22	36	1.95
40212496--40212631	41	3.4	41	69	14	115	35	25	15	24	1.94
40213541--40213598	22	2.6	22	78	7	55	3	12	13	70	1.28
40213609--40213642	5	6.8	5	93	0	59	55	0	2	41	1.15
40213636--40213663	11	2.5	11	100	0	56	46	7	0	46	1.30
40223255--40223294	7	5.9	7	94	2	64	70	0	27	2	1.01
40251334--40251360	2	13.5	2	100	0	54	48	0	0	51	1.00
40252251--40252283	2	16.5	2	93	0	57	48	51	0	0	1.00
40260103--40260133	2	16.0	2	93	6	55	51	0	0	48	1.00
40260553--40260597	23	2.0	23	81	0	54	62	15	0	22	1.33
40260788--40260845	22	2.6	22	81	7	64	41	17	5	36	1.72
40260824--40260919	21	4.8	19	87	9	147	34	15	11	38	1.84
40260824--40260919	40	2.4	40	96	0	174	34	15	11	38	1.84
40261098--40261132	6	5.8	6	93	0	61	65	0	17	17	1.27
40265557--40265591	6	5.8	6	89	0	52	68	2	11	17	1.31
40269047--40269076	16	1.9	15	93	6	51	43	13	16	26	1.85
40270278--40270561	113	2.5	112	78	7	263	35	17	21	26	1.95
40270501--40270624	63	2.0	63	83	3	160	37	16	20	24	1.93
40270563--40270993	229	1.9	228	84	2	578	31	18	24	25	1.98
40270584--40271008	114	3.7	113	76	9	373	30	18	24	26	1.98
40270620--40271123	229	2.2	229	80	3	552	30	18	23	27	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40271488--40271542	22	2.5	22	88	2	76	14	1	38	45	1.56
40271912--40271975	24	2.7	24	81	13	62	48	0	1	50	1.10
40272577--40272675	44	2.2	44	90	0	153	21	33	10	35	1.87
40274308--40274401	35	2.7	35	91	4	156	31	4	2	61	1.27
40274428--40274493	9	7.3	9	73	19	57	45	15	0	39	1.46
40274431--40274489	16	3.9	16	76	13	70	47	15	0	37	1.45
40274564--40274627	23	3.0	22	72	21	64	46	20	1	31	1.60
40274759--40274822	12	5.3	12	90	0	101	48	14	0	37	1.44
40274759--40274821	24	2.6	24	97	0	117	47	14	0	38	1.44
40274688--40274917	119	1.9	120	90	2	365	50	15	4	30	1.63
40274880--40274918	12	3.2	12	92	0	69	48	15	0	35	1.45
40275005--40275118	9	13.6	9	78	14	100	46	20	2	30	1.64
40274783--40275020	96	2.5	96	89	4	356	49	15	4	30	1.64
40275008--40275118	34	3.3	32	75	14	93	46	19	2	30	1.64
40275007--40275118	16	6.7	17	78	11	92	46	19	2	31	1.64
40274967--40275114	25	5.8	25	75	9	122	45	18	3	31	1.66
40280636--40280704	21	3.3	20	86	8	93	39	20	39	1	1.61
40281160--40281404	43	5.8	42	91	4	359	23	23	20	31	1.98
40281160--40281404	127	1.9	128	90	4	388	23	23	20	31	1.98
40285037--40285135	50	2.0	51	89	2	155	32	18	9	40	1.82
40287309--40287368	29	2.1	29	80	0	66	41	15	8	35	1.77
40287916--40287960	23	2.0	23	100	0	90	62	6	4	26	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40288501--40288714	105	2.0	105	99	0	419	41	17	5	35	1.72
40291364--40291411	19	2.5	19	96	0	87	47	20	0	31	1.50
40297285--40297319	12	3.0	11	88	12	52	22	0	25	51	1.48
40299048--40299088	20	2.0	20	100	0	82	34	24	9	31	1.88
40313744--40313794	25	2.0	25	100	0	102	25	11	31	31	1.92
40314231--40314348	26	4.3	26	80	10	110	40	8	27	23	1.83
40314275--40314341	31	2.2	31	97	0	125	38	11	23	25	1.89
40315503--40315555	25	2.1	25	85	0	70	26	24	20	28	1.99
40316262--40316461	43	4.7	42	83	2	202	29	27	17	26	1.98
40316301--40316486	43	4.3	43	81	8	200	27	28	17	26	1.97
40316262--40316486	85	2.6	86	81	5	240	28	27	17	26	1.98
40316262--40316488	43	5.3	43	80	5	158	29	27	17	25	1.98
40318101--40318292	87	2.2	87	89	0	287	43	17	7	31	1.76
40328190--40328244	22	2.3	24	81	12	69	41	3	36	18	1.68
40332400--40332430	15	2.1	15	93	0	53	35	9	9	45	1.70
40336576--40336627	15	3.6	15	80	12	56	44	0	1	53	1.11
40336525--40336708	59	3.1	59	65	21	148	41	2	7	49	1.42
40336705--40336746	15	2.7	16	82	14	52	45	0	2	52	1.13
40336696--40336737	15	2.9	15	82	10	52	47	0	0	52	1.00
40336513--40336743	120	1.9	120	95	1	419	41	2	6	50	1.40
40336680--40336990	154	2.0	154	96	0	568	46	4	3	45	1.40
40336846--40336880	18	2.0	17	88	5	52	45	0	0	54	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40336681--40336916	75	3.1	75	65	16	203	46	2	3	47	1.32
40337110--40337148	16	2.4	16	86	0	51	28	33	2	35	1.71
40337123--40337179	16	3.6	16	95	0	87	33	36	0	29	1.58
40337786--40337968	14	12.9	14	68	14	70	46	30	1	21	1.59
40337786--40337849	29	2.2	28	81	8	76	45	34	0	20	1.51
40337857--40337910	7	7.6	7	77	4	54	50	27	0	22	1.50
40337885--40337935	22	2.3	23	77	16	63	45	25	1	27	1.64
40338276--40338538	82	3.2	80	81	7	255	30	27	19	22	1.98
40338306--40338633	41	8.0	41	83	3	333	30	29	17	22	1.97
40347253--40347308	29	1.9	29	96	0	103	32	14	17	35	1.90
40349756--40349917	87	1.9	86	82	7	202	30	6	6	56	1.50
40353303--40353352	23	2.2	22	86	10	66	44	0	0	56	0.99
40353300--40353368	31	2.3	30	79	18	81	43	0	0	56	0.99
40353624--40353661	16	2.4	17	86	8	53	57	0	5	36	1.21
40353910--40353939	15	1.9	16	93	6	53	43	0	0	56	0.99
40357803--40357847	15	3.4	12	82	14	54	55	4	2	37	1.32
40358187--40358234	3	15.7	3	80	4	51	56	2	2	39	1.23
40359565--40359596	5	6.4	5	100	0	64	0	40	0	59	0.97
40359884--40360268	129	3.0	129	94	0	680	29	21	17	31	1.96
40359934--40360963	44	23.6	46	69	16	470	28	21	18	31	1.97
40359872--40360921	304	3.5	300	83	5	1178	28	21	18	31	1.97
40360412--40360747	129	2.6	128	89	2	501	28	22	18	30	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40360070--40360620	175	3.2	175	89	1	820	28	21	18	31	1.97
40360543--40360967	175	2.4	174	88	1	620	27	22	19	30	1.98
40359929--40360967	479	2.2	478	90	1	1627	28	21	18	30	1.97
40362127--40362165	9	4.8	8	84	15	53	10	12	0	76	1.01
40362109--40362164	24	2.3	24	87	9	78	12	14	0	73	1.11
40362118--40362166	10	5.6	9	85	14	59	10	12	0	77	0.99
40362118--40362166	17	2.8	17	82	17	57	10	12	0	77	0.99
40362984--40363020	6	5.8	6	93	6	56	0	13	0	86	0.57
40362984--40363021	7	5.7	7	96	3	62	0	13	0	86	0.56
40363063--40363112	9	5.7	9	97	2	93	10	0	10	80	0.92
40368787--40368833	24	2.0	24	95	0	85	10	4	38	46	1.58
40368895--40368967	28	2.6	28	77	14	80	49	10	10	28	1.72
40371791--40371825	15	2.2	16	95	5	63	5	20	0	74	1.02
40371792--40371896	20	5.4	20	70	25	59	7	19	0	72	1.14
40371808--40371882	20	3.8	18	81	11	69	8	18	1	72	1.17
40371791--40371870	15	5.7	14	68	24	53	7	20	0	72	1.08
40371798--40371905	41	2.7	40	76	16	107	8	20	0	70	1.19
40388552--40388584	11	2.8	12	90	9	50	27	6	0	66	1.15
40392373--40392438	34	1.9	34	93	0	114	34	22	7	34	1.83
40399006--40399097	38	2.4	38	82	5	107	28	29	21	20	1.98
40399266--40399311	23	2.0	24	82	4	58	32	23	0	43	1.54
40399450--40399484	3	11.7	3	100	0	70	65	0	0	34	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40399760--40399805	10	4.8	10	82	17	62	13	10	2	73	1.17
40400282--40400323	9	4.8	9	77	16	52	54	0	2	42	1.13
40404953--40404979	13	2.1	13	100	0	54	14	29	48	7	1.71
40406038--40406087	17	2.8	18	76	17	50	24	4	4	68	1.24
40406059--40406096	17	2.2	17	86	9	51	21	0	2	76	0.91
40410329--40410357	6	4.8	6	100	0	58	13	0	0	86	0.58
40411219--40411246	10	2.8	10	100	0	56	75	0	7	17	1.03
40414548--40414611	25	2.6	25	92	0	110	42	12	23	21	1.87
40424515--40424539	4	6.2	4	100	0	50	24	0	0	76	0.80
40427393--40427424	10	3.2	10	95	0	55	62	21	0	15	1.32

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