genome.fa.s1.2.7.7.80.10.50.1000.11.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: 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  11  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)
3961645--3961768	31	4.1	31	88	4	182	41	2	21	33	1.66
3961654--3961789	31	4.5	31	84	7	174	41	2	23	32	1.69
3976619--3976644	2	13.0	2	100	0	52	50	0	0	50	1.00
3983518--3983659	47	3.0	46	84	6	187	43	16	26	14	1.85
3983518--3983659	48	3.0	46	86	8	182	43	16	26	14	1.85
3984895--3985462	100	5.7	100	92	0	924	29	20	24	25	1.99
3984899--3985462	199	2.8	200	91	1	909	29	20	24	25	1.99
3984908--3985478	50	11.4	50	70	4	380	30	19	24	25	1.98
3985651--3985731	42	1.9	42	87	0	117	23	17	30	28	1.97
3985521--3985864	174	2.0	175	86	4	489	27	19	24	27	1.99
3987405--3987446	21	2.0	20	86	4	57	26	0	4	69	1.08
3993797--3993855	27	2.2	28	82	11	79	49	0	3	47	1.18
3995467--3995509	22	1.9	23	85	4	61	48	4	0	46	1.22
4002437--4002504	10	6.8	10	73	20	54	64	4	0	30	1.13
4002439--4002512	29	2.5	29	76	10	71	67	4	0	28	1.09
4006568--4006691	4	30.8	4	72	15	60	23	10	0	66	1.23
4012806--4012999	50	3.9	50	88	0	280	21	30	22	25	1.99
4012806--4012999	100	1.9	101	90	1	309	21	30	22	25	1.99
4013094--4013124	13	2.4	13	94	0	53	54	12	0	32	1.38
4019893--4020086	50	3.9	50	88	0	289	21	30	22	25	1.98
4019893--4020086	100	1.9	101	91	1	318	21	30	22	25	1.98
4020181--4020211	13	2.4	13	94	0	53	54	12	0	32	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4020423--4020479	30	1.9	30	86	10	82	31	24	5	38	1.78
4033423--4033448	2	13.0	2	100	0	52	50	0	50	0	1.00
4037102--4037169	30	2.3	31	85	10	88	47	14	8	29	1.75
4037887--4037925	2	19.5	2	100	0	78	51	0	0	48	1.00
4038238--4038636	46	8.6	47	93	1	626	37	14	19	29	1.91
4038261--4038636	93	4.0	93	95	0	637	36	14	19	29	1.91
4038215--4038636	139	3.0	140	91	1	661	36	14	18	30	1.91
4039478--4039607	43	3.0	42	80	16	158	30	28	19	22	1.98
4041421--4041494	23	3.2	23	90	3	96	43	18	8	29	1.79
4052738--4052832	28	3.5	28	84	8	124	31	10	25	32	1.90
4054017--4054242	46	4.9	46	93	3	384	28	26	9	35	1.87
4070558--4070666	37	3.0	37	93	2	186	36	16	22	24	1.94
4075735--4075815	20	4.2	19	75	10	74	61	4	1	32	1.25
4076645--4076680	10	3.7	10	85	7	56	22	0	5	72	1.05
4076645--4076693	19	2.5	20	90	6	73	26	0	6	67	1.14
4082197--4082239	22	1.9	23	90	4	70	48	2	2	46	1.27
4086979--4087017	21	1.9	20	84	5	51	38	2	0	58	1.12
4094899--4094972	4	18.5	4	100	0	148	25	0	24	50	1.50
4126511--4126594	27	3.1	27	91	0	132	17	22	36	22	1.94
4126522--4126613	27	3.4	26	86	5	121	22	20	34	21	1.96
4126511--4126613	54	1.9	54	84	7	138	22	21	33	22	1.97
4129206--4129287	38	2.2	38	97	0	155	39	2	3	54	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4129510--4129718	21	9.0	24	75	21	189	54	12	0	31	1.45
4129510--4129707	48	4.1	48	89	0	306	53	12	1	32	1.45
4129512--4129703	96	2.0	97	96	1	359	54	13	1	31	1.46
4129510--4129707	27	8.2	27	75	21	154	53	12	1	32	1.45
4129656--4129841	41	4.5	41	73	17	170	55	12	0	32	1.37
4129760--4129843	20	4.2	19	79	11	96	54	11	0	33	1.37
4129605--4129841	21	11.1	21	69	19	107	55	12	0	31	1.41
4129602--4129842	83	2.8	85	74	15	246	54	12	0	31	1.42
4129995--4130034	3	14.3	3	80	15	50	0	37	0	62	0.95
4129991--4130035	8	6.0	8	78	21	53	0	37	0	62	0.96
4129991--4130043	17	3.4	16	87	10	74	0	37	0	62	0.96
4129991--4130046	14	3.6	16	79	18	64	0	37	0	62	0.95
4139387--4139436	22	2.3	22	86	3	66	8	8	18	66	1.42
4140913--4140974	30	2.1	30	84	6	81	46	12	11	29	1.77
4140913--4140984	29	2.4	30	83	4	83	45	13	11	29	1.78
4152104--4152175	22	3.3	22	94	0	117	30	16	27	25	1.97
4156647--4156695	19	2.5	19	86	3	62	38	36	6	18	1.76
4156863--4156894	15	2.1	16	94	5	57	81	12	6	0	0.87
4157893--4157924	12	2.8	12	95	4	57	31	0	0	68	0.90
4157958--4158007	20	2.5	20	81	18	61	22	6	2	70	1.20
4158131--4158164	15	2.3	15	90	10	52	23	0	5	70	1.09
4158385--4158828	110	4.1	108	88	2	624	33	16	16	34	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4159088--4159120	13	2.5	14	90	9	52	72	0	27	0	0.85
4159734--4159777	20	2.0	22	83	12	56	9	6	36	47	1.62
4161058--4161123	11	6.0	11	72	0	51	63	16	4	15	1.46
4161058--4161116	22	2.7	23	71	7	59	62	15	5	16	1.49
4176580--4176685	9	11.6	9	88	4	140	33	30	9	27	1.88
4176692--4176826	17	7.4	17	66	19	67	49	14	3	31	1.61
4176683--4176830	37	4.0	37	90	0	224	47	15	4	32	1.64
4176683--4176735	20	2.9	18	75	8	54	49	16	1	32	1.57
4176836--4176891	24	2.3	24	93	0	94	32	28	0	39	1.57
4179232--4179273	20	2.1	20	100	0	84	66	0	4	28	1.12
4179502--4179547	22	2.1	22	95	0	83	32	15	13	39	1.85
4179497--4179550	22	2.3	25	75	18	69	35	12	11	40	1.79
4180479--4180522	17	2.6	17	92	0	70	22	2	29	45	1.65
4187013--4187167	30	5.2	30	76	13	124	33	18	3	43	1.68
4187013--4187158	61	2.5	62	84	6	178	32	18	4	44	1.69
4187487--4187527	17	2.4	16	84	15	55	82	0	12	4	0.81
4187614--4187651	16	2.5	15	91	8	60	81	5	10	2	0.94
4187665--4187709	22	1.9	25	86	13	69	64	20	13	2	1.38
4187836--4187881	14	3.7	13	75	18	53	76	0	23	0	0.79
4188207--4188266	17	3.5	17	86	4	84	33	18	10	38	1.84
4188239--4188409	52	3.2	53	82	9	199	32	10	10	46	1.73
4188290--4188388	17	5.8	17	74	8	85	28	11	11	49	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4188198--4188322	35	3.6	34	68	6	90	29	13	10	46	1.76
4188239--4188408	53	3.2	52	85	5	200	32	10	10	46	1.73
4188360--4188414	17	3.0	18	78	10	58	40	7	10	41	1.68
4188368--4188416	19	2.5	20	76	10	55	46	6	8	38	1.58
4188279--4188409	17	7.4	17	66	14	50	33	11	9	45	1.74
4192563--4192596	18	1.9	18	88	5	52	29	0	5	64	1.17
4198099--4198131	17	2.0	16	94	5	57	33	6	0	60	1.21
4199394--4199457	24	2.7	24	87	4	85	37	6	9	46	1.61
4203781--4203832	24	2.2	24	89	0	77	36	3	9	50	1.54
4211732--4211756	2	12.5	2	100	0	50	52	0	0	48	1.00
4212268--4212302	18	2.0	17	94	5	61	28	2	5	62	1.32
4213420--4213477	19	3.2	17	69	11	53	53	8	1	36	1.42
4214606--4214641	4	9.2	4	93	6	65	50	0	0	50	1.00
4223235--4223282	18	2.7	18	80	6	53	18	4	2	75	1.07
4223356--4223390	18	1.9	18	88	0	52	14	8	0	77	0.99
4223674--4223717	22	2.0	22	87	12	65	45	4	15	34	1.67
4235367--4235421	20	2.8	20	79	15	62	60	0	1	38	1.08
4235410--4235448	18	2.3	16	86	8	51	53	0	0	46	1.00
4235384--4235447	25	2.4	27	82	5	78	56	0	0	43	0.99
4240441--4240479	14	2.8	14	84	0	51	41	12	17	28	1.87
4241156--4241181	9	2.9	9	100	0	52	42	0	0	57	0.98
4248506--4248558	22	2.4	22	72	12	54	54	3	0	41	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4254269--4254554	158	1.8	154	85	8	400	27	7	8	56	1.56
4254429--4254468	13	3.0	13	85	3	53	25	2	2	70	1.13
4255099--4255139	21	1.9	22	85	14	59	48	2	2	46	1.28
4255237--4255266	14	2.1	15	93	6	53	60	0	0	40	0.97
4255230--4255267	13	2.8	13	82	17	51	52	0	0	47	1.00
4255360--4255412	23	2.3	23	87	6	72	45	0	7	47	1.31
4261498--4261539	13	3.1	13	83	16	50	52	4	0	42	1.22
4282137--4282199	3	21.3	3	96	3	119	68	0	0	31	0.90
4285170--4285267	33	2.9	33	80	4	115	19	27	19	33	1.96
4288448--4289193	373	2.0	376	84	8	1000	43	15	11	28	1.82

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