genome.fa.s20.2.7.7.80.10.50.1000.10.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: At_chr2
Parameters: 2 7 7 80 10 50 1000
Length:  61750188

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   

This is table  10  of  186  ( 22216 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)
3160162--3160191	9	3.2	9	90	9	51	33	10	0	56	1.32
3162927--3162974	19	2.5	19	89	0	69	10	29	14	45	1.78
3164509--3164999	147	3.3	146	86	2	642	32	15	24	27	1.96
3166276--3166318	16	2.5	17	81	11	52	23	9	9	58	1.58
3170372--3170432	30	2.0	30	83	0	77	31	22	8	37	1.84
3171536--3171576	18	2.3	18	91	4	66	21	7	4	65	1.37
3172997--3173054	31	1.9	31	82	3	73	44	15	5	34	1.69
3173849--3173965	47	2.4	48	83	8	150	59	5	1	33	1.29
3173945--3173974	10	2.8	11	90	10	53	73	0	0	26	0.84
3175918--3175971	17	3.4	17	70	15	60	53	0	1	44	1.11
3175909--3175970	31	2.0	31	96	0	115	56	0	1	41	1.09
3189833--3189864	15	2.1	16	94	5	57	62	0	0	37	0.95
3189832--3189921	19	4.9	19	76	12	73	62	3	1	33	1.19
3189859--3189924	10	6.6	10	75	5	62	60	4	1	33	1.26
3190001--3190077	19	4.3	19	69	16	58	61	3	0	35	1.15
3189832--3190077	9	27.0	9	66	17	73	56	4	1	37	1.28
3190934--3190969	19	1.9	18	88	5	54	33	5	0	61	1.19
3191082--3191122	21	2.0	21	85	9	57	41	4	4	48	1.46
3193286--3193320	18	1.9	18	88	0	52	37	2	2	57	1.29
3198525--3198689	78	2.2	78	87	3	237	27	7	1	63	1.30
3198619--3198725	34	3.1	34	64	17	78	30	8	1	58	1.38
3199860--3199907	20	2.5	20	86	3	62	64	2	6	27	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3199931--3199960	15	2.0	15	93	0	51	40	10	0	50	1.36
3200540--3200572	9	3.7	9	100	0	66	0	9	0	90	0.44
3201500--3201551	15	3.3	15	76	21	52	76	0	1	21	0.87
3201512--3201550	15	2.8	14	84	7	53	76	0	2	20	0.90
3201498--3201559	6	9.2	6	75	19	52	75	0	1	22	0.88
3201498--3201556	21	2.8	21	80	19	77	76	0	1	22	0.88
3205710--3205761	24	2.2	24	82	6	61	34	25	15	25	1.95
3207846--3207893	20	2.5	20	86	3	62	64	0	6	29	1.18
3207917--3207946	15	2.0	15	93	0	51	40	10	0	50	1.36
3219776--3219809	18	1.9	18	88	5	52	29	8	2	58	1.43
3220174--3220248	17	4.4	16	71	15	53	66	2	5	25	1.26
3220281--3220331	25	2.0	26	88	3	77	64	0	7	27	1.21
3220286--3220342	26	2.1	27	84	9	73	63	1	7	28	1.30
3220436--3220517	25	3.2	25	87	10	112	62	0	10	26	1.29
3220186--3220507	3	106.7	3	68	12	92	61	1	9	28	1.36
3220462--3220532	25	2.9	23	78	17	72	61	1	9	26	1.35
3220687--3220748	28	2.3	29	78	15	71	64	0	4	30	1.14
3220795--3220850	12	4.3	13	74	17	53	62	1	7	28	1.32
3221926--3221993	34	2.1	30	86	10	91	8	2	35	52	1.47
3222521--3222924	44	9.1	44	81	4	339	34	16	20	29	1.94
3222520--3222924	89	4.6	89	79	1	386	34	16	20	29	1.94
3223111--3223146	18	2.1	18	89	5	56	77	13	2	5	1.05
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3224378--3224635	68	3.7	70	79	9	260	27	8	2	62	1.37
3224361--3224635	141	2.0	141	83	8	355	26	8	2	62	1.38
3228146--3228190	22	2.2	20	88	8	63	62	0	11	26	1.29
3230917--3230958	13	3.0	14	80	19	52	57	0	2	40	1.12
3230922--3230964	14	3.1	14	80	6	52	62	0	2	34	1.08
3231350--3231396	22	2.0	22	88	8	67	44	2	4	48	1.34
3231362--3231405	22	2.0	22	86	4	61	45	4	2	47	1.35
3234259--3234283	10	2.5	10	100	0	50	0	8	0	92	0.40
3233839--3234397	277	2.0	275	97	0	1064	18	17	12	51	1.76
3250952--3251059	26	4.2	26	93	0	189	36	24	7	32	1.83
3258023--3258106	26	3.2	26	96	0	150	36	25	4	33	1.77
3259446--3259474	13	2.2	13	100	0	58	55	0	37	6	1.27
3267406--3267798	210	1.9	210	96	0	723	29	16	22	31	1.96
3267705--3267979	87	3.1	86	63	18	202	30	18	21	29	1.97
3267616--3267978	179	2.0	179	95	1	647	29	17	22	30	1.97
3267404--3268188	389	2.0	389	94	0	1363	28	17	22	30	1.97
3267792--3268226	210	2.1	210	93	0	744	28	19	22	29	1.98
3268440--3268525	45	1.9	45	88	4	129	30	12	30	26	1.93
3269539--3269721	72	2.5	71	83	7	213	48	6	18	26	1.71
3269583--3269688	34	3.0	34	87	6	131	51	7	19	20	1.71
3269539--3269721	39	4.9	38	84	7	214	48	6	18	26	1.71
3274240--3274298	31	1.9	31	86	6	84	18	11	13	55	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3275261--3275293	16	2.1	16	94	0	57	39	0	0	60	0.97
3275613--3275639	2	13.5	2	100	0	54	51	0	0	48	1.00
3276643--3276969	133	2.4	134	86	4	453	38	12	18	30	1.88
3277357--3277546	97	2.0	97	85	6	260	34	10	24	30	1.89
3277454--3277734	134	2.1	135	84	3	370	35	12	22	30	1.90
3293174--3293213	19	2.1	19	85	0	53	62	5	0	32	1.17
3293811--3293865	22	2.5	22	80	11	60	32	3	1	61	1.24
3293824--3293883	22	2.8	22	80	12	54	31	3	3	61	1.28
3294408--3294481	27	2.7	26	83	10	87	33	6	5	54	1.50
3294493--3294676	20	8.5	20	71	21	81	32	2	7	57	1.40
3294599--3294659	11	5.9	11	74	14	67	36	1	6	55	1.36
3294544--3294828	59	4.6	60	68	22	185	32	2	8	56	1.43
3294540--3294836	90	3.1	90	73	17	321	32	2	8	56	1.42
3294599--3294882	41	7.3	38	67	23	148	33	3	7	56	1.42
3294526--3294912	194	2.0	194	100	0	774	33	3	7	56	1.44
3294793--3294853	11	5.9	11	74	14	67	36	1	6	55	1.36
3294804--3294867	20	3.2	20	93	2	110	34	4	4	56	1.41
3298832--3298876	22	2.0	22	86	0	63	28	17	2	51	1.58
3307115--3307432	84	4.0	80	80	12	325	28	16	21	33	1.95
3307111--3307432	163	2.0	161	86	5	452	28	16	20	33	1.95
3307115--3307429	79	4.0	78	79	12	329	29	16	21	32	1.95
3307409--3307457	14	3.5	14	91	0	80	16	14	6	63	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3307330--3307523	101	1.8	103	84	8	266	25	14	18	40	1.89
3307460--3307579	64	1.9	64	85	0	168	25	20	24	30	1.98
3307576--3307609	13	2.5	14	85	4	52	17	8	5	67	1.37
3307807--3307954	63	2.3	63	89	0	233	28	16	29	25	1.97
3307933--3308037	45	2.3	45	90	3	158	31	19	19	30	1.96
3309551--3309605	22	2.5	22	80	11	60	32	3	1	61	1.24
3310147--3310202	14	4.1	14	73	13	53	35	8	1	53	1.43
3310157--3310222	27	2.5	27	85	7	91	34	6	4	54	1.45
3310201--3310270	19	3.2	23	68	22	60	32	1	7	58	1.34
3310161--3310274	27	4.7	25	74	19	84	34	4	5	56	1.42
3310207--3310276	21	3.2	21	75	18	72	32	1	7	58	1.34
3310223--3310276	19	2.7	20	85	8	65	33	1	7	57	1.37
3310172--3310285	23	5.0	22	72	22	92	34	2	7	56	1.40
3310207--3310295	43	2.0	43	81	10	101	32	1	8	57	1.37
3310342--3310432	20	4.3	20	88	10	137	32	5	6	54	1.49
3310346--3310432	44	2.0	42	93	4	147	33	5	5	55	1.48
3313428--3313506	33	2.4	33	82	0	95	16	27	26	29	1.97
3315360--3315442	36	2.3	35	81	6	87	34	10	21	32	1.88
3315592--3316345	398	1.9	398	84	1	1026	31	16	16	35	1.91
3316298--3316627	134	2.5	134	77	4	351	36	12	18	31	1.88
3317692--3318034	134	2.6	134	83	2	402	37	12	18	31	1.88
3319470--3319730	134	1.9	134	82	4	321	37	9	18	33	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3319708--3319754	23	2.0	23	83	0	58	40	17	8	34	1.79
3319604--3319887	157	1.8	157	83	4	376	37	10	17	33	1.85
3319440--3320022	291	2.0	291	99	0	1148	37	11	17	33	1.85
3319761--3320021	134	1.9	134	83	4	330	37	10	18	33	1.85
3319768--3320055	134	2.1	133	78	7	296	38	11	17	32	1.85
3324406--3326890	549	4.6	534	76	9	2012	34	16	16	32	1.91
3327153--3328934	948	1.9	930	86	3	2514	35	15	16	32	1.91
3330612--3331181	287	2.0	288	85	1	786	36	14	18	31	1.90
3331622--3332902	568	2.2	568	75	7	1265	34	14	17	33	1.90
3334036--3334669	346	1.8	347	81	4	787	33	20	15	30	1.93

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