genome.fa.s8.2.7.7.80.10.50.1000.140.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  140  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)
41223626--41223659	17	2.1	17	94	5	61	20	5	26	47	1.73
41238923--41238956	17	1.9	18	88	5	52	41	0	8	50	1.34
41239555--41240818	151	8.3	154	86	5	1643	31	9	7	52	1.61
41239545--41240817	301	4.2	303	87	5	1793	31	9	7	52	1.61
41240955--41241027	27	2.8	25	80	12	92	15	34	31	19	1.92
41245651--41245683	17	1.9	17	100	0	66	48	3	0	48	1.17
41248523--41248573	24	2.2	24	77	22	56	33	0	5	60	1.21
41248727--41248803	14	5.0	15	71	20	52	42	15	9	32	1.78
41248743--41248782	20	2.0	20	90	0	62	50	12	10	27	1.72
41248731--41248797	34	1.9	35	90	3	109	46	13	8	31	1.74
41248766--41248805	14	2.9	14	84	0	53	42	17	7	32	1.77
41250198--41250254	28	2.0	28	100	0	114	17	17	22	42	1.89
41255126--41255213	43	2.0	43	100	0	176	27	17	18	37	1.92
41259054--41259099	19	2.4	19	79	13	51	65	0	4	30	1.12
41265686--41265718	3	11.0	3	100	0	66	66	0	33	0	0.92
41267249--41267276	14	2.0	14	100	0	56	42	28	21	7	1.79
41268453--41268526	22	3.4	21	73	17	55	21	4	1	72	1.08
41268580--41268633	20	2.6	21	82	8	65	27	0	7	64	1.20
41268635--41268685	16	3.3	16	72	10	52	35	3	7	52	1.49
41269065--41269094	15	2.0	15	93	0	51	16	0	16	66	1.25
41280936--41281790	44	19.6	43	73	13	488	29	20	22	27	1.99
41280846--41281788	217	4.3	217	90	0	1377	30	20	22	27	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41280936--41281790	89	9.8	86	71	14	442	29	20	22	27	1.99
41281827--41281873	24	2.0	24	91	0	76	31	19	23	25	1.98
41283901--41283948	18	2.7	18	80	0	51	62	6	2	29	1.31
41285658--41285683	10	2.6	10	100	0	52	15	0	15	69	1.20
41286220--41286273	20	2.6	21	85	8	74	29	0	5	64	1.16
41289693--41289754	22	2.7	22	87	5	79	46	1	1	50	1.20
41289728--41289784	16	3.6	16	92	0	96	45	3	5	45	1.43
41290009--41290055	21	2.1	21	84	7	58	55	4	2	38	1.31
41290917--41290953	6	6.2	6	93	0	65	35	0	64	0	0.94
41290921--41290961	18	2.3	18	87	8	57	41	0	58	0	0.98
41292218--41292248	16	1.9	16	93	0	53	29	29	3	38	1.73
41293223--41293248	2	13.0	2	100	0	52	50	0	0	50	1.00
41298990--41299115	37	3.3	37	73	10	119	26	15	18	40	1.89
41298990--41299135	77	1.9	77	86	0	211	26	16	17	39	1.90
41300362--41300456	36	2.5	38	80	10	104	31	22	1	45	1.59
41303256--41303353	42	2.3	42	91	0	151	23	25	13	37	1.91
41303461--41303490	2	15.0	2	100	0	60	50	0	0	50	1.00
41308364--41308402	19	2.1	19	85	9	53	25	2	5	66	1.25
41314729--41314833	31	3.6	29	79	14	110	42	5	20	30	1.75
41314759--41314833	27	2.7	27	80	13	89	44	5	21	29	1.74
41315106--41315147	11	3.6	11	81	12	57	35	0	4	59	1.19
41334330--41334372	17	2.4	18	78	17	54	55	0	0	44	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41334749--41334811	31	2.0	31	87	6	90	61	0	1	36	1.05
41334786--41334819	17	2.0	17	88	0	50	64	0	0	35	0.94
41334766--41334831	29	2.2	30	89	5	98	60	0	3	36	1.12
41334809--41334872	30	2.1	29	83	11	76	59	0	4	35	1.18
41334749--41334893	41	3.5	40	89	6	202	59	0	3	37	1.15
41336885--41336920	17	2.1	17	100	0	72	11	11	11	66	1.45
41337248--41337311	33	1.9	34	87	6	96	43	17	4	34	1.69
41338094--41338150	23	2.6	21	83	16	71	17	7	21	54	1.66
41338113--41338165	23	2.3	23	100	0	106	20	7	26	45	1.78
41339352--41339727	48	7.8	48	97	0	698	50	6	7	35	1.58
41343078--41343286	92	2.3	91	85	5	269	46	3	3	46	1.37
41343214--41343261	26	1.9	25	84	16	64	45	0	2	52	1.12
41343436--41343477	15	2.7	16	82	14	52	45	0	2	52	1.13
41343427--41343468	15	2.9	15	82	10	52	47	0	0	52	1.00
41343580--41343614	18	2.0	17	88	5	52	45	0	0	54	0.99
41343411--41343727	157	2.0	157	96	0	589	47	4	3	44	1.41
41343850--41343917	16	4.2	16	92	0	109	39	32	1	26	1.65
41350009--41350486	261	1.8	261	83	4	642	39	10	14	35	1.80
41350257--41351047	308	2.6	295	79	6	813	40	9	13	36	1.78
41351640--41351672	17	2.0	17	88	5	50	42	0	0	57	0.98
41353000--41353037	18	2.1	18	90	0	58	42	7	36	13	1.73
41376311--41376353	22	2.0	22	85	0	59	32	2	6	58	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41378802--41378869	20	3.4	20	70	8	66	30	25	14	29	1.95
41378789--41378876	40	2.2	40	97	0	167	28	26	15	29	1.96
41378818--41378881	20	3.2	20	67	6	58	25	26	18	29	1.98
41379624--41379754	40	3.3	39	75	11	124	40	19	18	21	1.92
41381988--41382015	2	14.0	2	100	0	56	50	0	0	50	1.00
41382015--41382365	181	2.0	174	85	5	470	29	18	13	38	1.90
41384367--41384426	21	2.8	21	77	12	59	43	25	16	15	1.86
41393494--41393537	22	2.0	22	86	0	61	40	13	20	25	1.89
41402890--41403254	177	2.1	178	87	5	524	36	18	9	35	1.83
41403483--41403512	3	10.0	3	92	0	51	63	0	33	3	1.11
41404806--41405096	144	2.0	143	94	0	510	19	15	10	54	1.69
41405573--41405639	33	2.0	33	100	0	134	23	20	17	37	1.94
41406399--41406485	24	3.6	24	69	1	66	35	13	12	37	1.83
41406515--41406565	13	4.0	13	71	5	50	35	9	25	29	1.88
41408125--41408166	22	1.9	22	100	0	84	35	23	16	23	1.95
41409479--41409532	19	2.8	20	83	5	67	33	5	20	40	1.76
41415352--41415465	21	5.5	21	77	1	113	46	15	20	17	1.84
41415373--41415522	42	3.6	42	81	1	140	44	14	22	20	1.86
41415413--41415480	21	3.3	20	72	4	64	42	16	23	17	1.88
41417671--41417718	17	2.8	18	81	9	64	31	12	4	52	1.58
41427378--41427433	28	1.9	29	82	13	71	55	0	1	42	1.10
41428703--41428740	14	2.6	15	83	4	51	52	0	0	47	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41428742--41428788	17	2.6	18	86	6	60	46	4	2	46	1.34
41428763--41428811	21	2.3	21	80	16	57	40	0	2	57	1.10
41430494--41430567	27	2.8	26	73	8	69	63	2	2	31	1.22
41438169--41438208	3	13.3	3	100	0	80	67	0	0	32	0.91
41448089--41448151	28	2.3	26	83	5	72	46	26	3	23	1.68
41458416--41458460	23	2.0	23	81	0	54	60	4	4	31	1.37
41463878--41463910	16	2.1	16	100	0	66	42	27	0	30	1.56
41475965--41476008	17	2.6	17	82	7	54	34	2	2	61	1.21
41477689--41477736	22	2.2	22	85	7	62	35	10	4	50	1.56
41479899--41479939	20	2.0	21	85	4	57	65	4	2	26	1.25
41480744--41480778	15	2.4	15	90	4	54	48	0	8	42	1.33
41482196--41482328	66	2.0	66	86	2	187	36	19	9	33	1.85
41490380--41490424	19	2.4	19	100	0	90	37	13	4	44	1.64
41495999--41496128	34	3.9	32	77	10	127	40	2	13	44	1.56
41496215--41496862	126	5.2	126	86	2	847	38	16	16	29	1.90
41518178--41518213	18	1.9	18	88	5	54	38	16	11	33	1.84
41518958--41519036	13	6.2	13	73	5	54	43	18	3	34	1.69
41518927--41519023	50	1.9	50	91	0	158	39	18	4	38	1.70
41519798--41519847	22	2.3	22	92	0	82	8	24	36	32	1.84
41524588--41524640	16	3.4	16	71	10	56	66	3	5	24	1.31
41527625--41527830	46	4.5	46	92	1	337	29	21	15	33	1.94
41527899--41527945	19	2.3	21	85	7	62	42	12	0	44	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41529967--41529996	13	2.3	13	94	0	51	66	0	3	30	1.07
41536074--41536124	22	2.4	21	80	6	59	33	3	7	54	1.47
41537590--41537616	2	13.5	2	100	0	54	51	0	0	48	1.00
41540820--41540910	41	2.2	41	98	0	173	34	28	12	25	1.92
41544496--41544545	2	25.0	2	100	0	100	50	0	50	0	1.00
41550283--41550386	45	2.3	45	91	0	163	32	16	12	38	1.86
41571914--41572049	44	3.1	44	69	4	121	28	19	25	26	1.98
41571911--41572082	88	2.0	88	85	2	238	29	20	25	25	1.99
41572089--41572206	50	2.4	50	84	2	157	27	24	21	26	1.99
41572527--41572687	45	3.6	44	83	0	162	29	19	24	26	1.99

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