genome.fa.s1.2.7.7.80.10.50.1000.156.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  156  of  187  ( 22383 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)
46202357--46202399	22	2.0	22	95	0	77	30	11	9	48	1.71
46203374--46203634	89	2.9	89	85	3	330	26	6	9	56	1.57
46205825--46206120	93	3.2	93	87	3	425	42	2	17	37	1.61
46205889--46206036	43	3.3	43	65	18	111	39	2	21	37	1.65
46206923--46207142	109	2.0	108	87	2	316	34	18	17	29	1.94
46208870--46208907	6	6.0	6	88	11	58	0	18	0	81	0.69
46208870--46208905	14	2.8	13	91	8	56	0	16	0	83	0.65
46208870--46208907	13	3.0	12	88	11	58	0	18	0	81	0.69
46208932--46208972	7	6.1	7	77	11	50	14	0	4	80	0.87
46208929--46208970	14	3.1	14	86	10	61	14	0	7	78	0.95
46208936--46208972	19	1.9	19	89	10	58	13	0	5	81	0.86
46212430--46212747	110	2.9	110	87	2	455	34	18	17	29	1.94
46214626--46214661	10	3.4	10	85	14	54	5	0	36	58	1.22
46215015--46215653	44	14.7	43	73	9	343	26	21	21	30	1.98
46215013--46215303	129	2.2	130	85	4	372	26	21	21	29	1.99
46215013--46215653	131	4.9	129	74	10	372	26	21	21	30	1.98
46215013--46215520	175	2.9	174	82	7	554	26	22	21	29	1.99
46215147--46215522	87	4.3	87	75	7	307	26	22	22	29	1.99
46215772--46215909	43	3.2	43	66	15	122	22	21	26	29	1.99
46215668--46216524	87	9.9	87	91	2	1275	24	24	22	28	2.00
46215668--46216524	260	3.3	259	91	2	1355	24	24	22	28	2.00
46215668--46216524	347	2.5	346	90	2	1323	24	24	22	28	2.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46217816--46217913	7	13.7	7	96	3	178	13	13	0	73	1.10
46222775--46222813	18	2.1	18	85	9	51	64	0	5	30	1.15
46222891--46222953	14	4.4	14	78	9	65	55	0	3	41	1.16
46222902--46222956	25	2.2	24	87	9	74	58	0	1	40	1.09
46223025--46223078	3	18.0	3	100	0	108	66	0	0	33	0.92
46224515--46224540	11	2.4	11	100	0	52	57	0	0	42	0.98
46224911--46224942	16	2.0	16	93	0	55	18	12	3	65	1.38
46224901--46225896	134	7.4	135	83	8	1146	24	11	3	59	1.48
46225138--46225399	123	2.2	117	86	7	373	23	12	4	59	1.50
46225378--46225416	17	2.3	17	90	0	60	28	12	0	58	1.34
46225000--46225799	257	3.1	255	87	5	1052	23	11	4	60	1.48
46225633--46225668	17	2.1	17	100	0	72	11	11	5	72	1.28
46225704--46225749	17	2.6	17	86	6	56	19	13	2	65	1.37
46225785--46225828	17	2.6	17	92	0	70	31	4	2	61	1.28
46226033--46226068	2	18.0	2	100	0	72	50	0	0	50	1.00
46226398--46226489	6	15.7	6	82	6	109	34	15	2	47	1.57
46236726--46236763	18	2.1	19	85	5	51	34	0	5	60	1.19
46236783--46236828	22	2.1	22	84	8	58	47	2	2	47	1.26
46239045--46239101	3	18.7	3	92	3	96	66	0	1	31	1.02
46240615--46240692	30	2.8	28	74	16	88	23	2	8	65	1.34
46247013--46247129	35	3.3	35	82	1	135	15	9	31	43	1.78
46248542--46249031	250	2.0	250	86	4	702	26	31	13	28	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46253904--46254040	40	3.5	42	76	11	112	39	20	17	22	1.92
46254175--46254219	21	2.0	23	83	8	58	42	2	4	51	1.34
46254438--46254471	15	2.3	15	90	5	52	20	0	38	41	1.53
46254458--46254498	21	2.0	20	85	4	55	19	0	41	39	1.52
46254466--46254523	15	3.9	15	77	2	64	22	0	43	34	1.54
46254706--46254737	15	2.1	15	94	0	55	25	0	34	40	1.56
46254715--46254752	14	2.7	15	84	12	53	26	2	28	42	1.69
46254699--46254834	21	6.7	21	67	19	65	25	2	36	36	1.68
46254749--46254845	15	6.7	14	73	10	52	23	2	37	37	1.67
46258380--46258412	6	5.0	7	85	14	52	45	9	0	45	1.35
46258378--46258412	13	2.7	13	100	0	70	42	8	0	48	1.33
46258572--46258796	43	5.3	43	84	1	265	23	19	29	27	1.98
46258816--46258859	22	2.0	22	90	0	70	47	25	15	11	1.79
46260449--46260556	50	2.1	51	91	5	175	30	13	27	27	1.94
46270748--46270787	14	2.9	14	84	0	53	32	7	17	42	1.77
46270771--46270810	20	2.0	20	90	0	62	27	10	12	50	1.72
46270756--46270822	34	1.9	35	90	3	109	31	8	13	46	1.74
46280499--46280531	15	2.1	16	88	5	50	63	9	9	18	1.49
46286253--46286298	24	1.9	24	81	0	56	6	54	0	39	1.26
46286271--46286329	31	1.9	31	85	0	82	6	57	0	35	1.25
46286257--46286328	37	2.0	36	91	2	117	5	58	0	36	1.22
46286271--46286337	18	3.7	18	80	4	80	5	56	0	37	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46287637--46287694	30	1.9	30	92	0	98	37	22	13	25	1.91
46293552--46293610	30	2.0	30	96	0	109	37	8	23	30	1.85
46297444--46297692	69	3.6	69	85	3	288	44	25	6	23	1.77
46297444--46297692	138	1.8	138	82	5	324	44	25	6	23	1.77
46304049--46304108	21	2.8	22	72	7	61	36	26	18	18	1.94
46304558--46304591	17	1.9	18	88	5	52	35	23	0	41	1.55
46305188--46305257	28	2.3	32	78	14	85	48	5	1	44	1.35
46311382--46311410	2	14.5	2	100	0	58	51	0	0	48	1.00
46316673--46316750	3	26.0	3	100	0	156	33	0	0	66	0.92
46318209--46318270	26	2.4	26	94	0	106	35	17	25	20	1.95
46319140--46319235	10	9.7	10	71	18	76	59	0	5	35	1.20
46319138--46319198	30	2.0	32	90	6	99	57	0	3	39	1.15
46319180--46319247	29	2.3	29	76	20	70	58	0	7	33	1.26
46320928--46320963	2	18.0	2	100	0	72	50	0	0	50	1.00
46337389--46337449	14	3.9	16	72	22	58	31	19	8	40	1.81
46341468--46341497	15	2.0	15	93	0	51	23	26	13	36	1.92
46344385--46344459	23	3.3	23	90	0	114	17	20	29	33	1.95
46348886--46349270	87	4.4	87	91	1	578	29	22	23	24	1.99
46348886--46349270	173	2.2	174	90	1	594	29	22	23	24	1.99
46349297--46349433	40	3.2	43	75	13	147	35	22	22	18	1.96
46349410--46349837	87	4.9	87	92	0	730	32	22	22	22	1.98
46359635--46359661	2	13.5	2	100	0	54	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46360124--46360162	16	2.4	16	82	0	51	2	15	7	74	1.15
46365684--46365727	15	2.7	17	80	19	58	40	9	20	29	1.83
46378163--46378212	25	2.0	25	84	11	66	20	10	14	56	1.66
46378683--46378819	51	2.7	51	83	7	163	31	21	16	30	1.95
46381350--46381389	20	2.0	20	90	0	62	32	12	12	42	1.80
46382061--46382089	14	2.0	15	93	6	51	27	0	20	51	1.47
46382284--46382337	14	3.8	14	76	11	56	57	0	5	37	1.22
46382281--46382337	28	2.0	28	93	6	98	57	0	5	36	1.21
46384196--46384226	15	2.1	15	100	0	62	25	12	35	25	1.92
46384155--46384267	56	2.0	56	98	0	217	29	17	28	24	1.97
46384211--46384297	41	2.1	41	93	0	147	27	18	29	24	1.98
46387044--46387082	20	2.0	21	90	10	64	53	10	12	23	1.69
46388775--46388799	5	5.0	5	100	0	50	60	20	0	20	1.37
46390473--46390517	17	2.6	17	82	10	56	15	6	2	75	1.11
46393626--46393987	46	8.6	44	82	13	364	29	20	14	35	1.93
46393761--46393951	36	5.0	36	84	12	238	28	19	14	37	1.91
46393669--46393987	82	3.9	82	82	13	383	29	20	14	36	1.92
46393715--46393951	118	2.0	118	92	1	395	29	19	14	36	1.91
46401751--46401786	8	4.5	8	86	13	56	25	0	0	75	0.81
46404575--46404625	17	2.9	16	76	18	57	39	3	0	56	1.18
46405767--46405802	18	1.9	18	88	5	54	58	2	0	38	1.13
46405939--46405994	27	2.2	25	80	6	58	50	1	1	46	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46418602--46418641	21	2.0	20	85	5	53	65	0	2	32	1.06
46418725--46418783	24	2.6	22	76	10	55	52	1	6	38	1.38
46418669--46418989	104	3.1	102	86	7	448	52	4	8	34	1.51
46418770--46418823	20	2.7	20	76	0	63	51	1	7	38	1.41
46418816--46418987	56	3.1	55	71	20	162	52	4	7	35	1.49
46418879--46418927	20	2.5	20	86	0	71	55	0	8	36	1.30
46418915--46418962	16	2.9	16	84	9	60	52	4	6	37	1.46
46418725--46418885	48	3.3	48	70	19	141	51	3	8	36	1.49
46419527--46419568	3	14.7	3	85	9	61	73	0	0	26	0.83
46419525--46419576	12	4.6	11	88	7	61	76	0	0	23	0.78

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