genome.fa.s6.2.7.7.80.10.50.1000.40.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: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  51074515

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   

This is table  40  of  168  ( 20060 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)
10989860--10989906	2	23.5	2	100	0	94	51	0	0	48	1.00
10989966--10990008	12	3.4	12	75	12	50	48	0	0	51	1.00
10989971--10990008	12	2.9	14	84	15	62	42	0	0	57	0.98
10991752--10991794	15	2.9	14	80	10	50	62	2	0	34	1.08
10995654--10995691	10	3.8	10	86	10	51	47	0	10	42	1.38
10995650--10995691	19	2.2	19	87	8	59	47	0	9	42	1.36
11000957--11001015	29	2.1	27	81	12	66	32	5	6	55	1.48
11001601--11001631	16	1.9	16	93	0	53	51	6	3	38	1.44
11002205--11002354	76	2.0	76	94	2	266	50	17	12	20	1.77
11004274--11004353	40	2.0	40	100	0	160	47	17	17	17	1.83
11005229--11005258	16	1.9	15	93	6	51	80	6	0	13	0.91
11005201--11005263	27	2.3	26	81	7	72	73	4	1	20	1.11
11008586--11008636	13	3.7	13	79	10	57	76	1	0	21	0.88
11008585--11008638	14	3.9	14	80	9	65	75	1	0	22	0.89
11010045--11010079	18	1.9	18	88	11	54	65	0	17	17	1.27
11014415--11014442	13	2.2	13	100	0	56	39	0	21	39	1.54
11015297--11015386	43	2.1	43	97	0	171	26	25	20	27	1.99
11017487--11017539	21	2.5	21	93	0	88	15	24	41	18	1.89
11021662--11021729	25	2.7	25	81	4	93	35	23	16	25	1.95
11022617--11022658	21	2.0	21	95	0	75	50	14	26	9	1.73
11035243--11035383	57	2.4	59	83	11	182	27	22	25	24	2.00
11035507--11035635	67	1.9	67	88	3	197	24	17	30	27	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11038502--11038611	23	5.1	21	84	9	141	37	22	20	19	1.94
11038812--11038900	36	2.4	37	81	9	94	30	22	1	46	1.59
11038953--11038984	16	1.9	17	93	6	57	25	21	0	53	1.46
11039596--11039647	17	2.8	19	73	26	58	0	26	0	73	0.84
11039693--11039742	19	2.6	19	84	6	66	16	12	2	70	1.26
11039693--11039738	10	4.8	10	78	7	51	15	10	2	71	1.23
11043016--11043205	80	2.4	80	81	1	229	40	11	12	36	1.78
11055949--11056386	88	4.9	88	73	11	332	28	20	19	31	1.97
11055949--11056544	44	13.1	46	71	13	285	28	20	18	32	1.96
11056275--11056386	43	2.5	45	87	5	149	28	24	18	28	1.98
11056125--11056527	180	2.2	182	87	3	571	28	20	17	33	1.96
11057405--11057448	5	8.6	5	85	5	52	0	13	2	84	0.73
11057405--11057469	11	6.0	10	79	15	67	4	10	1	83	0.87
11061118--11061151	16	2.1	16	88	0	50	44	20	14	20	1.87
11091876--11091922	17	2.8	17	80	3	60	48	12	17	21	1.79
11102616--11102726	43	2.6	42	76	8	107	25	28	18	27	1.98
11103600--11103766	41	4.1	41	84	3	203	19	21	22	36	1.95
11103600--11103766	82	2.0	81	86	1	226	19	21	22	36	1.95
11104246--11104297	27	1.9	27	96	0	95	26	15	7	50	1.71
11115713--11115752	21	1.9	21	94	0	71	32	10	15	42	1.79
11117032--11117108	17	4.6	17	73	12	70	49	5	3	41	1.43
11119405--11119459	26	2.1	26	96	0	101	36	21	20	21	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11119612--11119677	27	2.4	27	82	5	71	22	13	24	39	1.90
11122389--11122443	16	3.4	16	89	0	56	27	32	1	38	1.67
11122401--11122458	16	3.6	16	90	0	89	29	34	0	36	1.58
11130467--11130500	17	2.0	17	94	0	59	11	38	29	20	1.88
11132084--11132115	17	1.9	16	93	6	55	40	9	6	43	1.62
11133976--11134016	18	2.3	18	95	0	73	63	14	9	12	1.52
11135886--11136256	104	3.6	103	93	1	600	19	19	30	30	1.97
11147613--11147661	21	2.3	20	80	13	55	24	26	20	28	1.99
11147775--11147810	17	2.1	17	94	0	63	30	16	22	30	1.96
11148313--11148346	17	1.9	18	88	5	52	26	2	8	61	1.40
11162854--11162899	21	2.2	21	84	7	58	32	4	6	56	1.45
11163680--11163714	14	2.5	14	90	0	61	60	0	0	40	0.97
11164243--11164441	99	2.0	97	98	1	380	42	15	8	34	1.76
11167474--11167663	51	3.8	50	78	8	215	31	26	16	25	1.96
11168786--11168842	4	14.0	4	89	10	89	22	0	0	77	0.77
11169306--11169343	17	2.3	17	86	4	51	60	5	26	7	1.46
11170849--11170937	6	14.5	6	87	4	124	14	3	3	78	1.01
11170964--11171006	3	14.3	3	95	0	77	30	2	0	67	1.03
11176883--11176924	20	2.0	20	95	4	75	69	0	14	16	1.20
11176883--11176923	7	5.9	7	88	11	66	70	0	14	14	1.16
11178154--11178428	128	2.1	128	95	1	489	29	20	24	25	1.99
11180279--11180321	3	14.3	3	100	0	86	32	0	0	67	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11182449--11182518	27	2.6	27	73	10	72	34	12	18	34	1.89
11188578--11188617	12	3.3	12	96	0	71	45	20	10	25	1.81
11188695--11188720	8	3.2	8	100	0	52	38	0	0	61	0.96
11189014--11189107	18	4.8	19	74	14	75	27	2	4	65	1.22
11189016--11189108	9	9.6	9	69	18	53	27	2	4	65	1.23
11189205--11189289	26	3.3	25	70	26	70	34	0	2	63	1.07
11189222--11189292	19	3.6	19	76	12	63	33	0	1	64	1.02
11189253--11189320	28	2.4	29	80	9	88	32	1	4	61	1.24
11189205--11189323	9	12.3	9	69	21	57	32	0	3	63	1.17
11189329--11189386	31	1.9	31	89	3	91	51	15	5	27	1.64
11197075--11197114	3	13.3	3	89	0	62	62	2	2	32	1.22
11208297--11208376	22	3.6	22	86	0	115	31	26	15	27	1.95
11215932--11216086	50	3.1	50	60	15	113	45	14	6	33	1.71
11215935--11216132	99	2.0	99	97	0	378	41	14	8	34	1.77
11220868--11220931	32	2.0	32	100	0	128	28	12	12	46	1.78
11221269--11221307	10	4.1	9	83	9	51	41	2	2	53	1.28
11221961--11222014	25	2.2	25	89	0	81	46	16	9	27	1.78
11222125--11222251	62	2.0	61	83	8	159	27	21	7	43	1.80
11228785--11228850	28	2.4	28	79	5	71	30	21	21	27	1.98
11228791--11228846	28	2.0	28	85	0	76	30	19	21	28	1.98
11229204--11229407	27	7.6	27	83	4	207	19	19	18	42	1.89
11229226--11229428	54	3.8	54	80	3	221	19	18	17	44	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11229205--11229404	81	2.5	79	81	6	240	19	19	19	42	1.89
11229205--11229428	81	2.8	79	78	8	236	18	18	19	43	1.88
11229226--11229407	27	6.7	27	85	0	229	19	19	17	43	1.88
11236012--11236065	22	2.4	22	84	12	65	66	3	1	27	1.19
11236013--11236076	26	2.5	25	82	2	74	65	3	1	29	1.17
11236086--11236126	21	2.0	21	85	0	55	56	4	7	31	1.48
11236532--11236617	44	2.0	45	90	4	140	15	22	4	58	1.55
11236710--11236843	19	6.7	21	78	10	77	40	14	6	38	1.73
11236710--11236767	22	2.6	22	81	7	64	41	17	5	36	1.72
11236746--11236856	19	5.8	19	86	0	168	37	14	9	38	1.78
11236746--11236849	38	2.7	38	96	0	190	38	13	8	39	1.75
11237004--11237083	28	2.9	28	88	1	117	25	22	26	26	2.00
11237203--11237252	26	2.0	26	96	4	93	36	28	24	12	1.91
11237428--11237595	27	6.3	26	80	8	178	16	19	22	42	1.88
11237428--11237595	54	3.1	53	78	8	196	16	19	22	42	1.88
11237455--11237593	53	2.6	54	86	3	192	15	19	21	43	1.88
11237425--11237584	80	2.0	80	90	2	250	16	20	23	40	1.91
11245401--11245425	12	2.1	12	100	0	50	24	36	24	16	1.94
11245586--11245626	18	2.3	18	91	0	64	41	21	7	29	1.80
11245595--11245662	9	7.4	9	79	9	66	42	19	10	27	1.83
11245754--11245802	23	2.1	23	96	0	89	14	0	36	48	1.44
11245759--11245811	13	4.3	13	79	13	67	16	0	39	43	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11261732--11261772	20	2.1	20	86	4	57	17	14	12	56	1.68
11262485--11262643	20	7.8	20	68	10	81	16	17	16	49	1.80
11262445--11262658	40	5.2	39	70	14	121	16	18	14	50	1.77
11262973--11263051	20	3.9	20	77	1	86	13	15	13	56	1.67
11263201--11263240	19	2.2	18	86	13	55	60	0	0	40	0.97
11267615--11267654	9	4.4	9	93	0	62	27	12	22	37	1.90
11267956--11268015	30	2.0	31	86	3	86	20	40	0	40	1.52
11272980--11273021	19	2.2	19	100	0	84	38	14	19	28	1.90
11273885--11273917	17	1.9	17	100	0	66	33	18	0	48	1.48
11293893--11293931	9	4.3	9	93	0	69	51	0	0	48	1.00

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