genome.fa.s1.2.7.7.80.10.50.1000.16.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  16  of  187  ( 22383 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)
5630177--5630809	44	14.5	45	68	11	228	31	18	21	28	1.97
5630426--5630840	175	2.4	174	88	1	614	30	18	21	29	1.97
5630775--5630859	44	1.9	44	85	0	116	29	17	24	28	1.97
5630426--5630893	175	2.7	175	84	1	528	30	17	22	29	1.97
5632535--5632632	3	32.7	3	77	4	99	32	4	2	61	1.26
5632523--5632603	15	5.4	15	84	0	81	30	4	1	62	1.24
5634304--5634349	18	2.5	18	82	10	58	19	0	8	71	1.11
5634469--5634864	110	3.6	110	90	3	584	31	14	19	34	1.92
5638152--5638335	59	3.1	59	66	20	173	42	2	7	47	1.42
5638151--5638338	61	3.1	61	69	17	201	43	2	6	47	1.42
5638182--5638367	54	3.2	53	66	24	133	44	1	4	49	1.33
5638140--5638370	120	1.9	120	97	0	435	42	2	6	48	1.41
5638332--5638373	15	2.7	16	82	14	52	45	0	2	52	1.13
5638323--5638364	15	2.9	15	82	10	52	47	0	0	52	1.00
5638307--5638623	157	2.0	157	96	0	589	47	4	3	44	1.41
5638489--5638530	15	2.7	16	82	14	52	45	0	2	52	1.13
5638658--5638762	44	2.5	40	76	15	113	31	29	4	34	1.78
5638656--5638765	45	2.6	44	81	8	131	31	29	5	33	1.80
5638744--5638781	16	2.4	16	90	0	58	34	34	0	31	1.58
5645235--5645268	17	1.9	18	88	5	52	55	20	2	20	1.56
5647388--5647422	15	2.3	15	90	0	52	48	5	31	14	1.67
5653321--5653347	8	3.4	8	100	0	54	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)
5655411--5655442	17	1.9	16	93	6	55	53	0	0	46	1.00
5657611--5657678	22	3.2	21	67	25	54	29	7	5	57	1.50
5659350--5659400	13	3.9	13	77	10	59	37	0	1	60	1.08
5659609--5659662	19	2.9	18	72	8	54	66	0	33	0	0.92
5662415--5662584	84	2.0	84	93	0	286	43	16	14	25	1.86
5663342--5663375	17	1.9	18	88	5	52	58	5	0	35	1.22
5671083--5671129	23	2.1	23	84	4	60	42	17	0	40	1.49
5672009--5672049	16	2.4	17	88	8	57	60	0	4	34	1.18
5684032--5684070	18	2.1	19	85	9	53	41	17	0	41	1.50
5703851--5703875	13	1.9	13	100	0	50	52	0	8	40	1.31
5707852--5707886	13	2.7	13	95	0	61	22	25	22	28	1.99
5714126--5714171	21	2.2	21	88	7	67	69	2	0	28	1.00
5716429--5716568	72	1.9	73	81	4	167	32	22	26	18	1.97
5716467--5716606	26	5.6	25	70	13	94	32	23	25	17	1.97
5720457--5720618	80	2.0	80	100	0	324	30	20	19	29	1.97
5723152--5723236	31	2.7	30	72	13	82	50	15	10	23	1.75
5726154--5726268	40	2.9	40	78	7	119	33	20	21	25	1.97
5726958--5727116	74	2.1	77	87	6	227	45	14	10	30	1.78
5729191--5729305	53	2.2	53	98	0	221	24	20	13	41	1.88
5729967--5730008	19	2.2	20	83	12	52	19	4	4	71	1.22
5729967--5730008	20	2.2	19	83	12	50	19	4	4	71	1.22
5730242--5730342	43	2.3	43	89	0	148	21	16	31	29	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5730419--5730460	22	1.9	22	95	0	75	40	28	21	9	1.84
5731558--5731588	11	2.8	11	90	0	53	67	0	0	32	0.91
5736554--5736644	34	2.7	34	78	11	98	37	7	1	53	1.37
5736599--5736642	16	2.6	18	75	14	56	36	6	0	56	1.26
5736723--5736759	2	19.0	2	94	5	67	51	0	0	48	1.00
5743096--5743148	27	2.0	27	100	0	106	33	11	18	35	1.87
5747309--5747343	2	17.5	2	100	0	70	48	0	0	51	1.00
5749558--5749582	6	4.2	6	100	0	50	84	0	0	16	0.63
5749999--5750074	23	3.3	23	76	12	84	31	25	19	23	1.98
5750300--5750338	18	2.2	17	86	13	53	46	20	0	33	1.51
5752954--5752979	7	3.7	7	100	0	52	73	15	0	11	1.11
5771498--5771625	61	2.1	61	78	11	138	39	9	15	35	1.80
5771530--5771651	61	2.0	61	85	7	169	33	9	18	39	1.82
5785491--5785529	18	2.2	18	86	9	53	48	2	0	48	1.15
5785561--5785588	6	4.7	6	100	0	56	50	0	0	50	1.00
5785667--5785722	23	2.4	23	82	5	69	44	3	1	50	1.29
5791231--5791286	28	2.0	28	96	0	103	21	23	12	42	1.86
5799599--5799681	43	2.0	41	85	4	112	48	7	7	37	1.59
5803888--5803926	2	19.5	2	100	0	78	51	0	0	48	1.00
5806598--5806642	23	1.9	24	86	4	65	57	4	2	35	1.31
5809571--5809606	16	2.2	16	90	0	54	55	2	0	41	1.14
5810763--5810820	2	29.0	2	100	0	116	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5810839--5810884	16	2.6	18	86	10	60	47	8	4	39	1.54
5810844--5810884	19	2.2	19	86	8	57	46	9	2	41	1.50
5821580--5821627	25	2.0	25	84	8	64	33	4	0	62	1.14
5823500--5823542	21	2.0	21	90	0	68	37	34	18	9	1.83
5831866--5831964	31	3.2	30	76	8	110	36	2	6	55	1.36
5832955--5833006	26	2.0	26	92	0	86	42	11	13	32	1.80
5832957--5833018	26	2.4	26	83	0	70	41	16	12	29	1.85
5833994--5834023	6	5.2	6	96	4	53	16	13	0	70	1.18
5836611--5836635	2	12.5	2	100	0	50	52	0	0	48	1.00
5842197--5842986	198	4.0	198	83	3	943	36	15	15	32	1.89
5844763--5844822	23	2.7	23	82	7	61	35	0	1	63	1.05
5847282--5847321	20	2.1	19	86	13	55	37	10	22	30	1.87
5851634--5851668	18	1.9	18	88	0	52	68	17	0	14	1.21
5853474--5853548	35	2.1	35	100	0	150	40	8	12	40	1.72
5853761--5853812	27	1.9	27	100	0	104	25	3	23	48	1.68
5853764--5853821	27	2.1	27	90	6	91	27	5	18	48	1.70
5854232--5854463	41	5.6	41	95	0	392	29	19	26	24	1.98
5854490--5854523	2	17.0	2	100	0	68	50	0	0	50	1.00
5856611--5856640	15	2.0	15	93	0	51	43	6	0	50	1.28
5856867--5856906	16	2.6	15	84	4	53	77	0	0	22	0.77
5857783--5857810	14	2.0	14	100	0	56	71	14	0	14	1.15
5857855--5857896	18	2.3	18	87	4	57	71	7	7	14	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5861641--5861843	52	4.1	51	80	12	244	34	13	23	29	1.92
5861704--5861897	46	4.3	46	78	15	217	37	13	21	27	1.92
5861664--5861860	98	2.0	98	94	0	349	34	13	22	28	1.93
5861750--5861860	52	2.1	53	90	5	172	36	12	22	27	1.91
5861824--5861932	37	3.0	37	93	2	186	36	16	22	24	1.94
5863758--5863914	41	3.8	41	91	0	242	33	29	19	17	1.95
5865104--5865202	42	2.4	42	87	0	135	28	26	9	36	1.87
5866532--5866595	32	2.0	32	100	0	128	18	31	25	25	1.98
5866603--5866671	26	2.7	26	76	10	79	17	21	21	39	1.93
5866653--5866731	23	3.3	23	70	8	59	15	25	22	36	1.93
5870367--5870405	20	2.0	20	89	0	60	25	5	0	69	1.09
5870396--5870454	20	2.7	21	79	12	57	42	3	1	52	1.28
5877817--5877945	64	2.0	64	100	0	258	26	13	18	41	1.88
5878096--5878158	29	2.2	29	97	0	117	22	9	12	55	1.65
5879390--5879714	161	2.0	162	86	3	456	28	13	24	34	1.93
5882493--5882525	15	2.1	16	88	5	50	3	21	0	75	0.93
5895381--5895411	7	4.4	7	100	0	62	61	12	0	25	1.32
5899391--5899421	15	2.1	14	94	5	53	0	9	0	90	0.46
5901805--5901990	37	5.0	37	92	2	293	27	20	14	37	1.91
5909590--5909618	2	14.5	2	100	0	58	51	0	0	48	1.00
5916463--5916494	2	16.0	2	93	0	55	46	0	3	50	1.17
5918260--5918619	44	8.2	44	68	2	220	26	25	20	28	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5918178--5918619	132	3.3	132	93	0	731	26	25	19	28	1.99
5918613--5918882	50	5.4	50	70	3	211	24	24	20	30	1.99
5918629--5918908	100	2.8	100	93	0	470	25	23	21	29	1.99
5920139--5920176	14	2.7	15	84	12	53	13	10	0	76	1.02
5920138--5920177	21	2.0	19	90	9	62	15	10	0	75	1.05
5927781--5927832	25	2.1	25	82	7	61	38	3	0	57	1.17
5928304--5928348	22	2.1	22	83	4	56	44	0	6	48	1.29
5929356--5929405	12	3.8	13	81	7	57	22	2	10	66	1.32
5930237--5930357	33	3.7	32	76	3	107	24	25	18	31	1.97
5930302--5930495	105	1.9	101	88	6	291	27	25	15	31	1.96

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