genome.fa.s4.2.7.7.80.10.50.1000.185.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: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

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   

This is table  185  of  198  ( 23681 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)
57522336--57522370	15	2.3	15	95	0	61	22	0	11	65	1.24
57524692--57524731	22	1.9	20	90	10	62	65	5	0	30	1.14
57529441--57529479	20	2.0	20	84	0	51	23	17	10	48	1.78
57538980--57539015	16	2.1	18	90	10	58	47	5	0	47	1.25
57545113--57545150	20	1.9	20	94	0	67	39	13	13	34	1.83
57558116--57558148	2	16.5	2	93	0	57	0	0	45	54	0.99
57561003--57561053	19	2.8	18	79	11	59	25	1	5	66	1.24
57564651--57564772	23	5.3	23	89	0	190	30	26	21	22	1.99
57564651--57564770	46	2.6	46	95	0	213	30	26	21	21	1.99
57567852--57567906	21	2.4	23	85	8	69	58	10	1	29	1.43
57568210--57568261	8	6.6	8	78	12	63	57	0	5	36	1.23
57568281--57568314	16	2.1	16	94	0	59	50	5	8	35	1.58
57568607--57568700	3	31.3	3	87	8	138	62	1	1	35	1.09
57569421--57569447	4	6.8	4	100	0	54	77	0	0	22	0.76
57574524--57574623	38	2.6	36	78	13	101	39	0	4	57	1.18
57574554--57574626	20	3.8	20	79	15	73	36	0	4	58	1.17
57574522--57574605	40	2.2	37	83	12	98	40	0	3	55	1.17
57574531--57574617	20	4.4	20	75	13	83	42	0	3	54	1.17
57574611--57574636	6	4.3	6	100	0	52	15	0	0	84	0.62
57576673--57576706	10	3.4	10	84	15	52	0	17	2	79	0.86
57578329--57578457	43	3.0	43	79	13	156	19	20	28	31	1.97
57581470--57581497	5	5.6	5	100	0	56	78	0	0	21	0.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57595410--57595453	17	2.6	17	85	0	61	72	2	0	25	0.96
57599254--57599287	14	2.3	15	90	5	52	50	0	2	47	1.16
57602191--57602227	9	4.1	9	92	0	65	45	13	10	29	1.77
57602555--57602591	20	1.9	19	89	10	58	24	32	0	43	1.55
57602564--57602639	20	4.0	20	73	16	56	25	28	0	46	1.53
57602717--57602797	17	4.6	17	72	20	69	38	3	2	55	1.31
57605666--57605783	41	2.8	41	80	11	134	29	28	21	20	1.98
57605625--57605789	43	3.9	41	78	12	156	29	29	19	21	1.98
57608070--57608134	32	2.0	32	100	0	130	27	18	9	44	1.80
57610386--57610439	13	4.1	13	76	11	56	44	5	0	50	1.25
57611164--57611218	21	2.4	23	85	8	69	58	10	1	29	1.43
57612855--57612889	18	2.0	18	94	5	63	74	5	14	5	1.19
57615504--57615535	5	6.4	5	100	0	64	18	0	0	81	0.70
57616319--57616355	3	12.3	3	88	0	56	32	2	2	62	1.23
57616444--57616480	17	2.1	18	90	5	58	43	5	5	45	1.49
57618161--57618195	18	1.9	18	88	11	54	31	0	5	62	1.18
57622779--57622822	21	2.2	20	83	4	52	29	6	9	54	1.58
57643566--57643633	33	2.1	30	82	15	75	39	1	2	55	1.24
57654324--57654628	108	2.8	108	92	1	488	32	20	17	29	1.95
57654915--57654971	13	4.4	13	75	16	64	54	1	1	42	1.21
57655058--57655085	13	2.2	13	100	0	56	60	7	0	32	1.24
57655250--57655315	3	22.0	3	96	0	123	66	1	0	31	1.01
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57657768--57657953	37	5.0	37	93	0	300	37	14	21	26	1.92
57657916--57658041	46	2.8	46	93	3	213	32	16	23	26	1.96
57659465--57659502	19	1.9	21	89	10	62	7	2	36	52	1.45
57662262--57662416	44	3.4	44	72	13	152	45	2	3	49	1.32
57662231--57662491	92	2.8	91	93	2	432	45	3	3	47	1.38
57662296--57662436	44	3.1	44	71	18	144	46	2	3	46	1.34
57662248--57662483	44	5.2	43	66	19	140	44	2	3	49	1.34
57662462--57662773	121	2.6	120	90	5	479	42	1	4	50	1.34
57662723--57662764	15	2.9	15	82	10	52	47	0	0	52	1.00
57669789--57669819	15	2.1	15	100	0	62	38	29	12	19	1.89
57670942--57670974	9	3.8	9	96	4	59	69	0	0	30	0.88
57670941--57670979	9	4.5	8	90	9	51	66	0	0	33	0.92
57683184--57683256	25	2.7	27	72	22	71	58	4	0	36	1.17
57683268--57683317	25	2.0	26	92	4	84	58	4	2	36	1.29
57690060--57690110	25	2.0	25	84	7	66	43	7	5	43	1.57
57699542--57699597	29	1.9	29	85	7	78	23	16	17	42	1.88
57703408--57703477	29	2.4	30	79	11	74	55	1	8	34	1.39
57704381--57704411	4	7.8	4	100	0	62	25	22	0	51	1.48
57708960--57709022	33	2.0	33	84	6	85	44	1	0	53	1.10
57710269--57710492	117	1.9	117	81	5	274	26	18	24	30	1.98
57714305--57714366	22	3.2	19	72	16	56	62	0	1	35	1.05
57714633--57714681	22	2.3	21	82	10	55	57	6	0	36	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57715366--57715437	26	2.7	26	85	6	83	52	2	2	41	1.30
57716007--57716038	2	16.0	2	100	0	64	50	0	0	50	1.00
57722501--57722540	18	2.2	19	86	4	55	57	2	5	35	1.34
57724451--57724818	90	4.1	90	93	0	574	25	24	23	26	2.00
57725948--57726326	51	7.4	51	91	0	499	26	28	18	26	1.98
57726375--57726443	21	3.3	21	95	0	120	46	13	36	4	1.62
57728927--57728954	6	4.7	6	100	0	56	82	0	0	17	0.68
57742345--57742372	14	2.0	14	100	0	56	35	14	14	35	1.86
57750140--57750219	41	2.0	41	85	5	108	37	23	0	38	1.55
57751245--57751282	13	3.0	13	88	11	53	60	0	0	39	0.97
57757538--57757573	16	2.2	16	100	0	72	25	0	36	38	1.56
57757559--57757667	44	2.6	40	74	17	112	32	6	27	33	1.82
57764319--57764344	13	2.0	13	100	0	52	61	7	30	0	1.24
57764308--57764383	39	1.9	39	97	0	143	52	14	26	6	1.66
57767015--57767066	27	1.9	27	100	0	104	21	26	26	25	1.99
57773610--57773640	9	3.3	9	95	4	53	70	0	0	29	0.87
57791836--57791865	14	2.1	14	100	0	60	40	30	6	23	1.80
57792134--57792159	2	13.0	2	100	0	52	50	0	0	50	1.00
57797862--57797894	12	3.0	11	91	8	50	42	0	9	48	1.35
57800742--57800900	43	3.7	43	85	2	194	23	17	27	31	1.97
57800902--57800939	18	2.1	18	95	0	67	18	26	26	28	1.98
57806216--57806249	14	2.4	14	90	0	50	38	2	8	50	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57808890--57808978	45	2.0	44	91	2	142	30	22	10	37	1.87
57820550--57820585	6	6.0	6	100	0	72	83	16	0	0	0.65
57829778--57829861	38	2.2	38	83	8	100	16	16	9	57	1.65
57830983--57831038	17	3.1	18	73	19	53	39	1	1	57	1.20
57832623--57832673	25	2.0	24	85	7	66	66	0	0	33	0.92
57839730--57839760	15	2.0	16	93	6	55	22	0	0	77	0.77
57841918--57842052	37	3.4	39	73	11	123	31	25	17	25	1.97
57841918--57842053	40	3.4	41	74	9	120	32	25	17	25	1.97
57842929--57842959	4	7.8	4	92	0	53	0	22	0	77	0.77
57843001--57843026	8	3.2	8	100	0	52	11	11	0	76	1.01
57843030--57843055	7	3.7	7	100	0	52	57	0	0	42	0.98
57846876--57846958	9	9.2	9	89	0	103	43	24	7	25	1.79
57846883--57846958	27	2.8	27	87	0	116	43	23	7	25	1.80
57847702--57847776	37	2.0	37	100	0	150	32	16	18	33	1.93
57847708--57847766	18	3.2	18	65	21	50	33	13	18	33	1.90
57849840--57849875	14	2.6	14	86	0	54	33	30	8	27	1.86
57850523--57850573	27	2.0	27	81	14	63	56	7	3	31	1.46
57853138--57853171	15	2.2	16	90	10	54	64	0	2	32	1.08
57863669--57863860	105	1.8	105	82	2	251	27	23	14	34	1.93
57884253--57884289	2	19.0	2	94	5	67	51	48	0	0	1.00
57886841--57886874	13	2.7	13	90	4	52	61	8	2	26	1.40
57895388--57895418	2	15.5	2	100	0	62	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57896484--57896522	20	2.0	20	89	0	60	48	5	0	46	1.24
57899428--57899517	25	3.7	24	71	16	78	51	1	2	45	1.21
57900590--57900618	2	14.5	2	100	0	58	48	0	0	51	1.00
57901245--57901316	36	2.0	36	94	0	126	37	4	12	45	1.61
57902661--57902693	12	2.8	12	100	0	66	36	9	0	54	1.32
57903560--57904183	105	5.9	105	86	3	749	33	17	19	29	1.95
57905307--57905346	20	2.0	20	90	0	62	17	17	5	60	1.54
57905332--57905726	56	7.1	56	88	4	568	24	20	0	54	1.47
57905449--57905532	26	3.2	26	61	12	62	22	16	0	60	1.35
57905459--57905541	28	3.0	28	63	19	75	22	15	0	61	1.34

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