genome.fa.s4.2.7.7.80.10.50.1000.148.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  148  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)
46948360--46948396	15	2.4	15	95	4	65	27	24	5	43	1.76
46948683--46948737	27	2.0	27	85	0	74	18	27	16	38	1.92
46951193--46951236	18	2.4	18	92	3	70	68	4	15	11	1.36
46952469--46952504	18	2.0	18	100	0	72	16	22	22	38	1.93
46953320--46953372	27	2.0	27	92	0	88	39	0	24	35	1.56
46953371--46953395	2	12.5	2	100	0	50	48	0	0	52	1.00
46971525--46971558	16	2.1	16	88	0	50	38	5	5	50	1.51
46971629--46971676	25	1.9	25	100	0	96	47	8	4	39	1.53
46971742--46971774	8	4.1	8	100	0	66	24	12	0	63	1.28
46972484--46972517	9	3.8	9	92	0	50	11	38	14	35	1.83
46974471--46974522	22	2.4	22	87	6	70	15	11	48	25	1.78
46975383--46975440	30	1.9	30	85	0	80	43	3	22	31	1.70
46975871--46976144	50	5.4	50	86	1	368	25	23	31	20	1.98
46975871--46976144	101	2.7	100	86	1	368	25	23	31	20	1.98
46977500--46977529	8	3.6	8	95	4	51	83	0	3	13	0.77
46977943--46977998	22	2.5	23	82	2	69	51	1	1	44	1.22
46977974--46978013	16	2.5	16	87	0	53	50	2	5	42	1.37
46978086--46978113	9	3.1	9	100	0	56	32	0	10	57	1.33
46978001--46978211	68	3.1	68	97	1	390	40	4	9	45	1.57
46978154--46978181	9	3.1	9	100	0	56	32	0	10	57	1.33
46978278--46978321	24	1.9	24	90	9	74	61	2	0	36	1.09
46978709--46978745	18	2.0	19	89	5	58	54	0	2	43	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46983798--46983847	9	5.4	9	79	11	57	64	4	0	32	1.12
46990803--46990840	20	1.9	20	88	0	58	28	23	10	36	1.88
46991929--46991988	3	20.0	3	92	0	102	3	30	0	66	1.07
46992132--46992202	33	2.2	32	80	11	85	22	8	23	45	1.80
46992269--46992325	10	5.6	10	78	17	64	57	1	1	38	1.19
46992269--46992357	20	4.4	19	74	13	72	55	1	5	38	1.31
46992269--46992357	10	8.8	10	72	16	51	55	1	5	38	1.31
46997647--46997693	19	2.4	18	80	13	58	42	4	2	51	1.33
46997715--46997769	28	2.0	28	82	10	69	40	1	0	58	1.09
46998472--46998510	16	2.5	15	83	4	51	46	2	0	51	1.14
46999888--46999925	18	2.1	18	85	14	51	42	0	0	57	0.98
47000401--47000459	22	2.8	22	75	14	70	49	0	0	50	1.00
47000424--47000481	25	2.3	26	82	8	66	48	1	3	46	1.29
47001276--47001322	23	2.0	23	87	0	67	14	4	6	74	1.17
47010083--47010168	26	3.3	25	88	6	118	39	10	15	34	1.81
47011287--47011335	25	1.9	26	87	4	73	38	8	6	46	1.58
47011474--47011551	31	2.5	31	80	13	90	51	5	1	42	1.32
47011503--47011551	20	2.7	18	77	22	57	51	4	2	42	1.32
47020460--47020501	21	1.9	23	85	9	61	57	2	0	40	1.12
47020504--47020533	11	2.6	11	94	5	51	60	0	3	36	1.14
47024121--47024148	8	3.5	8	100	0	56	57	0	0	42	0.99
47024155--47024223	31	2.2	31	84	5	84	27	27	10	34	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47024395--47024439	2	22.5	2	100	0	90	51	0	0	48	1.00
47034294--47034411	58	2.0	58	100	0	236	34	15	15	34	1.89
47040640--47040673	16	2.1	16	88	0	50	17	5	5	70	1.28
47045279--47045312	17	1.9	18	88	5	52	61	5	0	32	1.20
47045740--47045805	24	2.8	23	86	6	80	57	4	3	34	1.34
47051033--47051266	41	5.7	41	89	1	351	23	28	20	28	1.98
47051959--47051998	2	20.0	2	100	0	80	50	0	0	50	1.00
47055816--47055905	25	3.6	25	93	0	144	33	22	26	17	1.96
47055794--47055906	25	4.6	25	87	1	138	32	22	26	18	1.97
47056214--47056243	15	1.9	16	93	6	53	43	13	6	36	1.70
47061241--47061314	37	2.0	37	100	0	148	40	16	5	37	1.71
47064559--47064751	25	7.7	25	70	13	78	22	26	18	32	1.97
47072038--47072083	24	1.9	24	86	0	65	17	26	21	34	1.95
47072075--47072142	25	2.7	26	80	8	70	17	23	20	38	1.93
47072205--47072256	25	2.1	25	85	7	70	25	25	17	32	1.97
47073879--47073964	14	6.4	13	73	11	50	75	6	4	12	1.16
47078936--47078977	2	21.0	2	100	0	84	50	0	0	50	1.00
47079144--47079170	14	1.9	14	100	0	54	25	0	0	74	0.83
47085141--47085206	31	2.1	31	81	10	73	28	4	1	65	1.21
47085243--47085293	24	2.2	23	93	6	86	39	7	0	52	1.30
47087027--47087053	14	1.9	14	100	0	54	44	18	7	29	1.77
47092675--47092845	72	2.4	72	85	4	240	55	13	5	25	1.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47093269--47093316	18	2.7	18	96	0	87	35	12	16	35	1.87
47095945--47096018	25	3.0	25	89	0	103	47	25	24	2	1.65
47098687--47098713	6	4.5	6	100	0	54	55	29	14	0	1.40
47099600--47099740	40	3.6	40	74	6	126	26	17	25	29	1.98
47100176--47100213	19	2.0	19	100	0	76	21	10	26	42	1.85
47106235--47106270	18	2.0	18	88	0	54	25	2	13	58	1.49
47108097--47108165	35	2.0	35	94	0	120	27	21	23	27	1.99
47108293--47108377	32	2.8	30	81	10	91	28	14	27	30	1.95
47112172--47112233	26	2.3	27	83	8	83	30	14	33	20	1.93
47121305--47121373	36	1.9	36	82	8	88	24	14	15	44	1.84
47122494--47122574	27	3.0	26	78	12	92	30	16	30	22	1.95
47124901--47124970	22	3.2	22	93	0	113	30	17	27	25	1.97
47125984--47126050	30	2.3	30	82	7	75	38	22	2	35	1.70
47126024--47126078	28	1.9	30	82	10	71	41	27	0	30	1.56
47130074--47130099	13	2.0	13	100	0	52	30	7	23	38	1.83
47131030--47131091	25	2.5	25	86	2	90	24	24	6	45	1.76
47138040--47138082	21	2.0	21	86	0	59	53	16	11	18	1.72
47138241--47138276	18	2.0	18	94	0	63	38	13	0	47	1.44
47142106--47142144	18	2.2	17	86	13	53	33	0	20	46	1.51
47142370--47142468	23	4.3	23	92	0	171	23	21	25	30	1.99
47144361--47144423	28	2.2	28	84	15	78	38	4	15	41	1.69
47144719--47144750	2	16.0	2	100	0	64	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)
47144928--47145657	363	2.0	363	95	0	1307	29	20	15	35	1.93
47156372--47156404	14	2.2	15	89	10	50	39	18	6	36	1.75
47161094--47161143	23	2.2	23	100	0	100	26	8	18	48	1.75
47164321--47164370	19	2.6	19	93	0	82	24	30	32	14	1.94
47168924--47169091	84	2.0	84	90	0	264	22	34	4	38	1.75
47169313--47169747	228	1.9	219	90	5	683	21	37	13	27	1.91
47180122--47180167	13	3.5	13	81	0	56	39	15	15	30	1.88
47183047--47183144	34	2.6	40	79	18	145	54	9	8	28	1.61
47186636--47186833	100	2.0	97	90	4	308	33	19	19	28	1.96
47187468--47187532	30	2.1	31	85	2	87	56	1	9	32	1.40
47190947--47191177	50	4.6	50	85	1	277	21	29	22	27	1.99
47193394--47193500	21	5.4	20	71	16	80	21	15	6	56	1.62
47193439--47193511	36	2.0	37	86	2	103	21	17	8	52	1.71
47200577--47200628	24	2.2	24	92	0	86	23	30	1	44	1.64
47201570--47201597	14	2.0	14	100	0	56	28	7	14	50	1.69
47202595--47202628	17	2.0	17	100	0	68	41	11	11	35	1.78
47204615--47204662	21	2.3	21	85	0	60	37	14	43	4	1.65
47205195--47205281	18	4.7	18	66	20	54	41	2	4	51	1.35
47205160--47205287	56	2.3	56	97	1	240	41	3	4	50	1.39
47205276--47205328	11	5.1	11	74	19	51	41	3	1	52	1.30
47208119--47208167	25	2.0	25	83	0	62	30	14	28	26	1.95
47208581--47208625	21	2.0	22	83	8	56	40	20	0	40	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47226667--47226704	18	2.1	18	95	0	67	50	21	13	15	1.78
47228996--47229141	75	2.0	72	89	4	220	24	23	20	31	1.98
47235250--47235274	2	12.5	2	100	0	50	0	0	48	52	1.00
47242502--47242561	6	10.0	6	100	0	120	0	50	0	50	1.00
47248112--47248170	22	2.7	23	79	10	61	47	0	1	50	1.11
47255330--47255387	29	2.0	29	96	0	107	31	43	6	18	1.77
47257606--47257683	38	2.1	38	100	0	156	39	20	15	24	1.91
47265812--47265851	21	1.9	21	89	0	62	20	12	15	52	1.74
47268882--47268906	13	1.9	13	100	0	50	40	8	8	44	1.63
47271639--47271674	14	2.6	14	95	0	63	41	0	2	55	1.14

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