genome.fa.s8.2.7.7.80.10.50.1000.17.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   

This is table  17  of  190  ( 22705 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)
4849549--4849749	34	6.2	33	68	22	81	44	15	1	38	1.58
4849427--4849830	81	4.9	81	89	6	512	44	13	2	40	1.56
4849854--4849910	25	2.3	25	84	0	69	43	14	5	36	1.67
4854142--4854414	43	6.3	43	79	2	289	21	17	31	29	1.96
4854142--4854393	129	2.0	129	84	3	328	22	17	30	28	1.97
4854162--4854416	86	3.0	86	88	1	359	23	17	31	27	1.97
4854184--4854478	86	3.4	86	81	6	312	22	18	30	28	1.97
4854593--4854635	22	2.0	22	95	0	77	41	27	20	9	1.83
4858153--4858178	13	2.0	13	100	0	52	15	30	15	38	1.88
4859641--4859671	3	10.3	3	100	0	62	32	0	0	67	0.91
4859798--4859830	2	17.5	2	87	12	52	51	0	0	48	1.00
4859878--4859927	2	25.5	2	95	4	93	48	0	0	52	1.00
4860079--4860138	26	2.3	25	80	8	66	38	10	0	51	1.35
4860093--4860135	12	3.4	12	78	12	50	41	11	0	46	1.40
4860093--4860127	14	2.5	14	85	0	52	42	8	0	48	1.33
4862464--4862509	23	2.0	23	82	0	56	41	10	2	45	1.51
4862477--4862537	31	2.0	31	83	6	79	39	13	3	44	1.60
4869750--4869781	2	16.5	2	93	6	57	46	0	0	53	1.00
4874729--4874771	18	2.2	20	88	8	63	25	2	6	65	1.30
4876059--4876903	296	2.8	299	75	10	765	37	13	8	40	1.76
4875755--4877616	840	2.2	838	79	7	1960	36	13	9	39	1.78
4878703--4878737	2	17.5	2	88	11	54	51	2	0	45	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4879819--4879884	20	3.3	20	74	4	80	19	18	9	53	1.71
4879814--4879895	39	2.1	39	97	0	155	19	20	7	52	1.70
4886244--4886281	11	3.5	11	89	7	60	68	0	31	0	0.90
4886307--4886345	19	2.0	21	85	10	55	23	0	10	66	1.22
4887672--4887714	21	2.0	21	100	0	86	58	0	9	32	1.30
4887662--4887845	75	2.4	79	78	11	191	38	5	7	48	1.53
4888475--4888549	33	2.3	33	82	8	93	0	30	0	69	0.89
4888502--4888641	22	6.4	22	75	14	121	0	28	0	71	0.86
4888543--4888643	4	26.0	4	78	15	97	0	27	0	72	0.85
4888503--4888641	68	2.1	67	87	6	201	0	28	0	71	0.86
4888922--4888962	21	2.0	21	85	9	57	26	0	7	65	1.18
4888924--4888976	22	2.4	23	81	12	58	26	0	5	67	1.12
4894544--4894589	18	2.6	18	86	6	58	13	6	8	71	1.29
4894639--4894663	3	8.3	3	100	0	50	32	0	0	68	0.90
4897375--4897422	24	2.0	24	95	0	87	45	10	12	31	1.76
4903654--4903695	18	2.3	19	83	8	59	54	4	9	30	1.53
4906267--4906293	8	3.4	8	100	0	54	11	0	11	77	0.99
4908323--4908410	18	5.2	17	75	12	65	46	11	11	30	1.75
4908326--4908394	18	3.9	17	75	7	66	50	13	10	26	1.72
4908447--4908659	18	11.6	18	71	14	127	44	9	14	31	1.77
4909170--4909208	16	2.4	16	83	8	53	0	17	10	71	1.12
4909172--4909232	14	4.7	13	82	17	74	0	16	11	72	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4909362--4909417	3	18.3	3	92	3	94	0	33	1	64	1.04
4909500--4909550	24	2.2	23	85	3	66	11	13	5	68	1.37
4909855--4910017	30	5.6	29	81	5	177	38	4	21	35	1.73
4909849--4910017	59	2.9	58	78	7	198	39	4	20	34	1.74
4910205--4910952	74	9.8	75	85	5	800	34	20	17	27	1.95
4910205--4910934	151	4.8	147	82	8	736	33	21	17	27	1.95
4911078--4911254	75	2.3	77	86	6	252	37	17	15	29	1.90
4912126--4912167	9	4.9	9	77	11	52	0	0	11	88	0.53
4912125--4912168	12	3.6	12	87	6	70	0	0	11	88	0.51
4912126--4912179	13	4.5	12	78	21	51	0	3	11	85	0.73
4912122--4912179	24	2.4	25	83	16	77	0	5	10	84	0.77
4917474--4917517	22	2.0	22	81	0	52	0	27	0	72	0.85
4924793--4924880	18	5.2	17	75	12	65	47	10	11	30	1.73
4924796--4924864	18	3.9	17	75	7	66	52	11	10	26	1.69
4924770--4924895	36	3.5	36	76	8	96	49	10	11	28	1.72
4924937--4925005	18	3.7	18	77	12	77	37	11	13	37	1.80
4924939--4925018	38	2.2	35	84	13	99	37	10	16	36	1.82
4925013--4925062	18	2.8	18	90	0	64	56	10	12	22	1.65
4925025--4925075	18	3.0	17	88	8	77	50	13	9	25	1.72
4925026--4925083	17	3.4	17	83	9	73	46	12	12	29	1.77
4925680--4925713	14	2.3	15	95	5	61	0	20	11	67	1.21
4925872--4925906	3	11.3	3	93	6	61	0	34	0	65	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4925989--4926039	24	2.2	23	85	3	66	11	13	5	68	1.37
4926192--4926225	9	3.7	9	88	7	50	0	14	0	85	0.60
4926336--4926483	30	5.0	29	81	6	181	39	2	22	35	1.68
4934651--4934707	30	1.9	30	82	13	73	43	3	3	49	1.36
4934886--4934920	13	2.7	13	95	0	61	42	20	14	22	1.88
4936387--4936422	16	2.2	16	100	0	72	25	0	36	38	1.56
4936658--4936692	18	2.0	17	88	5	52	54	0	0	45	0.99
4936545--4936863	159	2.0	157	95	1	575	43	3	5	47	1.40
4936797--4936838	15	2.7	16	82	14	52	52	2	0	45	1.13
4936806--4936847	15	2.9	15	82	10	52	52	0	0	47	1.00
4943914--4944010	20	5.1	19	73	12	74	41	10	7	41	1.67
4943953--4943990	17	2.3	17	90	4	60	47	10	2	39	1.52
4943892--4944009	57	2.1	57	80	3	130	42	9	6	41	1.63
4943953--4944012	17	3.4	17	76	13	59	45	8	5	41	1.56
4944036--4944067	16	2.0	16	100	0	64	31	12	12	43	1.80
4944859--4944895	14	2.6	14	86	0	56	10	24	43	21	1.84
4944944--4944986	12	3.6	12	75	12	52	2	34	39	23	1.67
4945462--4945500	8	4.8	8	81	6	51	82	0	12	5	0.83
4945509--4946132	81	7.8	80	82	8	666	33	20	17	29	1.95
4946988--4947067	1	80.0	1	70	0	52	0	8	6	85	0.76
4946994--4947065	16	4.3	16	79	8	81	0	8	6	84	0.77
4947000--4947066	9	7.7	9	82	12	68	0	7	7	85	0.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4947000--4947065	34	1.9	35	87	3	98	0	7	7	84	0.77
4947000--4947066	25	2.6	26	86	9	84	0	7	7	85	0.76
4952739--4952823	20	4.4	20	70	16	63	38	10	8	42	1.69
4952778--4952814	17	2.3	17	86	9	51	43	10	5	40	1.63
4952847--4953099	36	7.0	36	75	12	202	43	11	14	31	1.80
4952846--4953097	72	3.5	72	79	11	225	43	11	14	30	1.81
4952862--4953099	17	13.3	17	70	13	140	43	10	13	31	1.79
4953184--4953226	20	2.2	20	100	0	86	37	9	9	44	1.69
4953187--4953452	17	14.8	17	71	12	149	41	9	15	33	1.79
4953207--4953461	36	7.1	36	74	9	166	40	9	16	33	1.80
4953471--4953511	17	2.4	17	88	12	57	41	7	17	34	1.77
4954003--4954048	14	3.3	14	90	0	65	8	26	45	19	1.79
4954219--4954296	28	2.6	30	82	12	88	6	21	0	71	1.08
4954229--4954280	18	2.7	20	82	14	72	3	25	0	71	1.03
4954406--4954470	21	3.0	21	76	10	60	0	13	10	75	1.05
4954406--4954457	23	2.4	22	83	6	61	0	13	7	78	0.94
4954399--4954470	24	3.0	25	75	19	71	0	16	9	73	1.08
4954846--4955006	29	5.4	29	78	5	117	40	4	22	32	1.73
4954883--4954991	29	3.7	29	85	11	159	38	1	27	32	1.67
4954883--4955007	59	2.1	59	82	10	157	39	4	24	32	1.74
4955378--4956015	81	8.0	79	82	9	660	33	20	17	29	1.95
4955375--4955921	161	3.4	159	86	6	695	33	20	16	29	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4956872--4956944	18	3.9	18	87	8	94	1	2	6	89	0.64
4956872--4956948	19	4.1	18	85	11	100	1	2	7	88	0.66
4956884--4956948	9	6.9	9	86	10	94	1	0	9	89	0.56
4956902--4956957	29	1.9	29	85	0	76	1	3	8	85	0.78
4956872--4956946	1	75.0	1	78	0	78	1	2	6	89	0.63
4968003--4968052	23	2.2	22	82	7	55	52	4	12	32	1.57
4970335--4970399	27	2.4	27	100	0	130	13	27	36	21	1.92
4970444--4970615	10	17.9	10	74	21	90	69	0	30	0	0.89
4970457--4970634	44	4.5	39	82	15	199	68	0	31	0	0.90
4970443--4970608	44	3.8	45	83	14	215	68	0	31	0	0.90

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