genome.fa.s8.2.7.7.80.10.50.1000.32.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  32  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)
9216359--9216408	25	2.0	25	96	0	91	22	16	0	62	1.33
9218659--9218733	20	3.7	19	76	13	60	70	1	22	5	1.15
9225901--9225947	24	2.0	24	84	16	62	51	17	0	31	1.46
9226691--9226761	2	39.5	2	70	25	52	52	2	0	45	1.15
9228078--9228114	16	2.3	16	90	0	56	16	24	0	59	1.37
9233522--9233554	2	16.5	2	93	0	57	51	3	0	45	1.16
9239120--9239339	106	2.1	106	93	0	370	31	17	17	32	1.94
9239548--9239608	30	2.0	30	84	6	79	65	9	6	18	1.43
9239713--9239756	19	2.4	19	88	3	63	70	0	6	22	1.11
9239813--9239841	14	2.0	15	93	6	51	68	6	0	24	1.13
9243924--9243967	2	22.0	2	100	0	88	50	0	0	50	1.00
9257582--9257607	2	13.0	2	100	0	52	50	0	0	50	1.00
9259830--9260033	102	2.0	102	95	1	365	25	19	31	23	1.98
9261221--9261248	13	2.2	13	100	0	56	53	0	0	46	1.00
9262640--9262685	20	2.3	20	92	0	74	52	15	4	28	1.61
9262648--9262691	20	2.2	20	83	0	52	52	9	4	34	1.54
9266347--9266377	7	4.4	7	91	0	53	25	12	16	45	1.83
9266651--9266715	22	3.0	22	75	4	71	18	20	15	46	1.84
9267340--9267373	7	4.7	7	85	7	50	41	2	0	55	1.15
9277519--9277573	21	2.7	21	73	18	53	30	1	1	65	1.13
9278099--9278143	19	2.5	19	92	7	76	28	2	0	68	1.01
9278110--9278152	19	2.3	19	87	0	59	27	4	0	67	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9278520--9278565	21	2.1	22	84	11	60	65	2	2	30	1.16
9280304--9280343	21	1.9	21	94	0	71	40	17	17	25	1.91
9280591--9280646	22	2.5	22	85	5	69	32	16	19	32	1.94
9283280--9283376	25	3.8	25	78	9	99	30	21	27	19	1.98
9284398--9284436	18	2.0	20	90	9	64	46	0	0	53	1.00
9284399--9284441	15	2.8	16	86	10	63	48	0	0	51	1.00
9286352--9286388	20	2.0	19	85	15	51	37	8	0	54	1.30
9287973--9288054	40	2.0	40	100	0	164	26	2	21	48	1.63
9287991--9288067	21	3.8	21	66	10	61	28	2	19	49	1.62
9295602--9295632	2	15.5	2	100	0	62	48	0	0	51	1.00
9295762--9295858	36	2.7	35	77	17	94	29	9	20	40	1.84
9304835--9304892	25	2.4	24	83	11	73	13	27	25	32	1.94
9304906--9304980	25	3.0	25	77	11	82	21	25	21	32	1.98
9306788--9306903	24	4.8	23	75	8	79	16	31	21	30	1.95
9306859--9306915	25	2.3	24	75	3	60	21	29	21	28	1.98
9307807--9307837	16	1.9	16	93	0	53	32	6	3	58	1.40
9309230--9309295	20	3.4	19	72	8	62	19	16	9	54	1.68
9309250--9309306	19	2.9	19	71	5	60	19	21	7	52	1.69
9309225--9309306	39	2.1	39	97	0	155	20	19	7	52	1.70
9313039--9313072	6	5.5	6	86	6	50	41	58	0	0	0.98
9313038--9313073	13	2.8	13	87	4	56	38	61	0	0	0.96
9319747--9319928	43	4.3	43	86	3	251	31	29	18	20	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9319876--9320013	42	3.2	43	79	15	160	34	29	15	21	1.94
9321015--9321077	32	2.0	32	100	0	126	42	15	12	28	1.84
9323069--9323109	21	2.0	21	90	0	64	24	0	43	31	1.54
9323124--9323440	147	2.1	147	97	0	598	30	15	16	37	1.89
9324081--9324197	41	2.9	41	81	12	134	26	28	23	22	1.99
9324229--9324365	40	3.5	40	81	5	152	18	20	21	39	1.93
9330058--9330116	29	2.0	29	96	0	109	27	5	27	40	1.77
9332835--9332876	14	3.2	13	86	13	59	59	9	2	28	1.41
9334240--9334290	20	2.6	20	84	9	61	35	9	19	35	1.85
9343469--9343615	43	3.4	43	80	3	154	27	17	26	29	1.97
9349013--9349055	18	2.5	17	85	7	52	11	37	32	18	1.87
9355264--9355291	10	2.8	10	100	0	56	17	0	0	82	0.68
9356951--9356999	20	2.4	21	80	16	59	46	0	12	40	1.41
9375291--9375390	42	2.4	42	91	0	164	37	12	27	24	1.90
9377991--9378016	9	2.9	9	100	0	52	7	0	0	92	0.39
9378061--9378146	3	28.3	3	85	2	109	31	4	2	61	1.29
9378136--9378174	15	2.5	15	83	8	51	30	7	0	61	1.24
9378183--9378233	16	3.4	16	75	20	56	29	3	5	60	1.38
9380908--9380954	24	2.0	23	87	4	67	76	4	8	10	1.13
9381902--9382077	55	3.1	53	70	20	165	49	5	1	43	1.36
9381742--9382098	119	3.0	119	95	1	637	51	5	1	42	1.31
9384869--9384908	18	2.2	18	95	0	71	55	5	35	5	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9385886--9385945	22	2.5	24	78	15	70	15	13	10	61	1.56
9387238--9387262	12	2.1	12	100	0	50	40	8	0	52	1.31
9388923--9388951	2	14.5	2	100	0	58	0	48	0	51	1.00
9394114--9394176	22	2.9	22	80	0	72	30	9	20	39	1.84
9394176--9394251	33	2.3	33	84	4	91	30	21	21	27	1.98
9394240--9394530	87	3.3	87	79	1	280	29	25	21	22	1.99
9394240--9394530	29	10.0	29	70	4	113	29	25	21	22	1.99
9394317--9394511	58	3.4	58	78	1	176	28	26	23	22	1.99
9394498--9394563	34	1.9	34	84	0	87	28	25	25	19	1.99
9398745--9398793	22	2.3	22	85	3	64	63	4	4	28	1.31
9399001--9399062	19	2.9	21	79	20	67	64	1	4	29	1.23
9401494--9401529	17	2.2	16	90	5	54	80	0	13	5	0.88
9405279--9405311	9	3.8	9	88	8	50	63	0	0	36	0.95
9406565--9406594	15	1.9	16	93	6	53	56	3	0	40	1.16
9406736--9406766	11	2.7	11	95	5	53	70	0	0	29	0.87
9408410--9408504	20	4.8	20	73	0	64	52	10	20	16	1.73
9408410--9408504	40	2.4	40	74	0	100	52	10	20	16	1.73
9408507--9408604	21	4.9	21	71	15	82	52	6	19	22	1.68
9408507--9408605	20	4.9	20	66	16	60	52	6	19	22	1.67
9415126--9415157	8	3.9	8	95	4	55	46	0	0	53	1.00
9415200--9415241	13	3.2	13	84	15	59	76	0	16	7	1.00
9417842--9417893	20	2.6	20	81	6	61	46	3	17	32	1.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9420489--9420586	42	2.3	42	79	10	119	16	18	17	47	1.82
9432974--9433052	29	2.7	28	79	11	79	77	3	5	13	1.08
9432977--9433040	17	3.7	17	79	8	67	76	4	3	15	1.08
9432974--9433052	23	3.4	23	81	8	72	77	3	5	13	1.08
9432974--9433052	6	13.5	6	75	7	65	77	3	5	13	1.08
9435054--9435100	17	2.7	18	83	12	62	68	0	31	0	0.90
9435131--9435157	6	4.5	6	100	0	54	14	14	51	18	1.76
9441840--9441898	24	2.5	24	97	0	109	13	40	0	45	1.43
9444681--9445048	75	4.8	75	76	12	381	31	28	19	21	1.97
9444835--9444970	27	4.8	27	89	5	191	31	29	20	18	1.96
9446313--9446499	101	1.8	101	88	5	288	24	17	26	31	1.97
9446309--9446495	51	3.7	51	82	5	229	25	17	26	31	1.97
9446464--9446488	12	2.1	12	100	0	50	24	16	28	32	1.96
9446506--9446594	45	2.0	45	88	0	133	25	16	24	32	1.96
9449013--9449069	22	2.7	21	76	7	62	73	12	3	10	1.21
9455937--9455971	18	1.9	18	88	0	52	77	5	2	14	1.07
9456332--9456589	45	5.8	45	81	2	218	39	17	20	23	1.92
9456290--9456545	89	2.9	91	73	9	224	39	17	19	23	1.92
9456987--9457131	73	2.0	73	88	0	218	33	6	19	40	1.76
9459577--9459635	3	19.7	3	100	0	118	67	0	0	32	0.91
9460564--9460643	23	3.5	23	73	11	65	28	13	30	27	1.94
9463355--9463397	23	1.9	23	85	4	61	58	0	6	34	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9464402--9464520	26	4.6	26	90	4	168	26	16	20	36	1.94
9471335--9471381	18	2.6	19	83	12	64	23	14	0	61	1.33
9471581--9471622	18	2.3	18	87	0	57	26	9	4	59	1.48
9478252--9478602	45	7.8	45	95	0	612	26	16	27	29	1.97
9478252--9478691	135	3.3	135	89	2	620	27	16	26	29	1.97
9478718--9478868	51	3.0	51	89	0	239	31	13	24	30	1.94
9478726--9478889	51	3.2	51	85	1	231	31	14	25	29	1.94
9478698--9478884	102	1.8	102	88	2	286	29	14	24	31	1.95
9480568--9480606	18	2.1	19	90	4	62	28	15	2	53	1.55
9481620--9481665	16	2.9	16	73	23	51	41	4	28	26	1.74

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