genome.fa.s9.2.7.7.80.10.50.1000.11.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: 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  11  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)
5158527--5158633	20	5.3	20	85	4	135	38	4	16	40	1.70
5158450--5158614	87	1.9	87	82	0	204	38	5	16	38	1.72
5158527--5158652	40	3.2	40	80	6	139	37	4	18	39	1.72
5158527--5158652	60	2.1	60	82	5	148	37	4	18	39	1.72
5158749--5158920	20	8.6	20	69	6	107	34	6	15	43	1.73
5158747--5158849	39	2.6	39	78	1	116	33	5	15	44	1.70
5158729--5158899	79	2.2	80	77	6	186	37	7	14	40	1.73
5158789--5158920	60	2.2	59	77	4	140	34	6	15	43	1.74
5158977--5159027	20	2.5	20	80	0	57	39	0	17	43	1.49
5159143--5159183	20	2.0	20	95	0	73	43	0	21	34	1.53
5159250--5159302	20	2.7	19	80	16	63	41	3	15	39	1.65
5159295--5159342	20	2.4	20	86	6	62	39	2	18	39	1.63
5159572--5159690	20	5.9	20	75	5	107	40	5	15	38	1.70
5159564--5159669	40	2.7	40	80	0	122	40	4	16	38	1.69
5159573--5159688	60	1.9	60	89	3	180	41	4	16	37	1.68
5159576--5159708	60	2.2	61	84	6	173	41	5	14	39	1.68
5159572--5159708	20	6.8	20	75	5	98	40	5	14	39	1.68
5160196--5160241	22	2.1	22	83	0	56	65	0	10	23	1.24
5171374--5171399	13	2.0	13	100	0	52	15	0	0	84	0.62
5173870--5173929	4	15.0	4	100	0	120	50	25	0	25	1.50
5175564--5175606	5	8.6	5	94	0	68	0	2	23	74	0.93
5189786--5189837	24	2.2	24	89	0	77	25	42	1	30	1.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5189804--5190710	48	18.9	48	77	8	685	25	51	2	20	1.61
5189806--5190710	96	9.4	96	86	5	1061	24	51	2	20	1.61
5190286--5190562	27	11.4	25	64	22	94	26	50	4	18	1.66
5198685--5198717	3	11.0	3	87	12	50	63	0	0	36	0.95
5202861--5202928	27	2.6	27	78	2	75	41	8	0	50	1.34
5202931--5202960	11	2.7	11	94	0	51	86	10	3	0	0.67
5203533--5203598	19	3.6	18	70	13	53	46	1	9	42	1.44
5203533--5203585	18	2.8	19	77	8	56	49	0	9	41	1.35
5206763--5206829	25	2.7	25	88	0	98	34	17	26	20	1.96
5207644--5207668	5	5.0	5	100	0	50	20	0	0	80	0.72
5210140--5210385	51	5.0	51	65	22	146	42	17	16	22	1.89
5210158--5210252	45	2.1	45	90	3	147	43	17	15	23	1.88
5210158--5210264	45	2.6	41	83	8	128	42	18	16	22	1.89
5210002--5210434	141	3.0	140	87	6	571	42	17	16	22	1.89
5210289--5210407	51	2.3	51	79	2	132	44	16	15	22	1.86
5210607--5210693	40	2.2	40	83	4	104	43	20	6	28	1.78
5212310--5212358	26	2.0	24	84	8	62	61	2	0	36	1.08
5223360--5223428	24	2.9	23	81	14	86	21	26	4	47	1.69
5231151--5231188	16	2.4	17	82	13	53	42	0	2	55	1.14
5237109--5237154	19	2.6	18	77	19	51	58	2	0	39	1.10
5237940--5238009	31	2.3	31	82	5	79	45	4	21	28	1.70
5240091--5240200	44	2.5	44	96	0	202	30	13	22	32	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5258695--5258750	22	2.5	23	74	8	62	57	8	8	25	1.58
5265366--5265406	15	2.6	16	81	11	50	12	9	7	70	1.33
5283631--5283665	18	2.0	18	88	5	54	54	0	0	45	0.99
5285390--5285456	34	1.9	35	90	3	109	46	10	8	34	1.70
5291056--5291095	18	2.2	19	86	4	55	42	12	0	45	1.42
5301221--5301339	60	2.0	60	91	3	195	52	10	0	35	1.42
5301453--5301501	22	2.2	23	79	13	59	4	26	0	69	1.06
5301628--5301731	27	3.9	27	89	0	154	19	29	25	25	1.98
5305702--5305732	5	6.2	5	92	0	53	0	64	0	35	0.94
5330863--5330900	2	19.0	2	100	0	76	50	0	0	50	1.00
5340226--5340299	36	2.1	36	94	0	130	18	13	24	43	1.86
5349204--5349281	33	2.3	35	78	10	81	73	3	15	7	1.21
5349251--5349291	20	2.0	20	90	4	64	73	2	24	0	0.96
5349719--5349824	37	2.7	38	82	5	133	25	16	25	33	1.96
5355453--5355640	25	7.7	24	69	15	91	19	25	19	36	1.95
5380896--5380923	13	2.2	13	100	0	56	42	25	7	25	1.80
5383774--5383807	17	2.0	17	88	11	52	47	2	5	44	1.42
5397466--5397500	11	3.2	11	92	8	54	91	8	0	0	0.42
5399083--5399133	13	3.9	13	77	10	59	37	0	1	60	1.08
5407055--5407099	18	2.5	18	92	0	72	26	44	13	15	1.83
5407262--5407306	18	2.5	18	82	7	56	35	13	13	37	1.84
5410516--5410559	11	3.9	11	88	5	61	68	4	0	27	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5411014--5411048	2	17.5	2	100	0	70	48	0	0	51	1.00
5416835--5416861	11	2.5	11	100	0	54	22	7	18	51	1.70
5418273--5418449	91	1.9	92	91	3	295	45	2	4	48	1.35
5418273--5418411	47	3.0	44	68	18	122	45	2	5	46	1.39
5418520--5418561	15	2.9	15	82	10	52	50	0	0	50	1.00
5418671--5418705	18	2.0	17	88	5	52	45	0	0	54	0.99
5418504--5418818	155	2.0	157	94	1	553	47	4	3	44	1.40
5418866--5418960	45	2.1	44	88	5	138	33	26	6	33	1.82
5418939--5418992	16	3.4	16	89	0	63	37	31	0	31	1.58
5422861--5422908	25	1.9	25	82	0	60	45	18	10	25	1.81
5435182--5435324	62	2.3	62	93	0	250	24	22	26	26	2.00
5437256--5437387	67	2.0	67	90	3	212	27	31	19	21	1.98
5439734--5439807	2	37.0	2	91	0	121	50	2	0	47	1.15
5443227--5443274	17	2.9	17	90	3	71	27	0	18	54	1.44
5444498--5444636	46	3.0	46	84	6	183	35	9	24	30	1.87
5464901--5464947	20	2.2	22	77	11	53	65	8	8	17	1.44
5465287--5465343	25	2.3	25	81	6	62	31	10	0	57	1.32
5465416--5465449	16	2.2	16	89	5	52	35	2	2	58	1.28
5467671--5467697	7	3.9	7	100	0	54	70	0	0	29	0.88
5472033--5472439	101	4.0	101	88	1	584	28	23	15	32	1.95
5472074--5472412	33	10.1	33	63	12	125	29	23	15	31	1.95
5475826--5475878	25	2.2	24	89	3	79	35	22	24	16	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5476180--5476259	22	3.6	22	91	3	133	47	23	2	26	1.64
5479462--5479544	30	2.8	29	80	14	80	43	1	2	53	1.21
5493208--5493270	30	2.1	30	96	0	117	57	12	3	26	1.51
5495577--5495621	19	2.3	20	76	3	56	46	2	0	51	1.13
5501942--5501981	20	2.0	20	100	0	80	35	30	20	15	1.93
5517755--5517817	25	2.5	25	84	7	65	38	7	22	31	1.83
5517766--5517817	25	2.0	26	88	3	79	38	5	23	32	1.78
5519565--5519634	30	2.4	29	75	11	72	48	10	1	40	1.45
5521210--5521234	12	2.1	12	100	0	50	32	0	0	68	0.90
5522157--5522209	27	2.0	26	82	7	63	43	3	1	50	1.30
5523843--5523885	12	3.5	13	78	12	54	76	0	0	23	0.78
5527673--5527700	2	14.0	2	100	0	56	50	0	0	50	1.00
5552333--5552370	13	2.9	13	84	0	58	28	7	21	42	1.81
5554033--5554077	2	22.5	2	90	0	72	46	2	0	51	1.13
5564945--5565900	115	8.4	115	81	5	1048	31	19	23	25	1.98
5564945--5565900	229	4.2	228	84	4	1117	31	19	23	25	1.98
5564945--5565900	457	2.1	454	83	4	1181	31	19	23	25	1.98
5566211--5566253	14	3.0	14	86	3	50	20	0	37	41	1.53
5570642--5570667	8	3.2	8	100	0	52	88	0	0	11	0.52
5570782--5570960	9	19.6	9	68	17	70	32	1	2	62	1.19
5570798--5570894	41	2.4	41	86	8	130	35	2	2	60	1.20
5570874--5570899	8	3.2	8	100	0	52	26	0	0	73	0.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5570782--5570894	20	5.8	20	69	18	78	33	2	1	61	1.20
5570838--5570962	16	6.9	18	67	18	55	31	0	3	64	1.14
5570969--5571143	88	2.0	88	83	6	221	39	6	14	39	1.72
5571966--5571992	12	2.2	12	100	0	54	14	0	7	77	0.97
5576524--5576587	21	3.1	21	66	20	62	32	23	15	28	1.95
5579647--5580201	295	1.9	297	84	2	758	27	19	15	37	1.92
5582994--5583265	134	2.0	134	97	0	517	31	12	17	37	1.88
5612906--5612930	8	3.1	8	100	0	50	0	12	0	88	0.53
5615462--5615496	18	2.0	17	94	5	61	57	0	0	42	0.99
5616301--5616335	18	2.0	17	94	5	61	42	0	0	57	0.99

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