genome.fa.s3.2.7.7.80.10.50.1000.93.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: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  45765648

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   

This is table  93  of  150  ( 17918 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)
29253574--29253996	219	1.9	218	88	0	630	27	21	24	25	1.99
29253753--29254039	87	3.3	87	89	0	430	27	23	23	25	2.00
29255864--29255919	20	2.7	21	83	13	80	35	3	3	57	1.34
29258346--29258394	21	2.3	21	96	3	89	48	20	10	20	1.78
29266431--29266508	23	3.4	23	77	13	97	42	26	11	19	1.85
29266424--29266516	46	2.0	46	95	0	168	43	24	11	20	1.85
29268120--29268147	8	3.5	8	100	0	56	25	0	35	39	1.56
29272718--29272750	5	6.6	5	100	0	66	60	0	0	39	0.97
29274479--29274527	20	2.5	20	96	0	89	53	0	24	22	1.47
29281554--29281641	42	2.1	42	81	4	108	26	20	27	26	1.99
29282742--29282786	21	2.1	21	100	0	90	33	20	13	33	1.91
29287358--29287387	14	2.1	14	93	0	51	36	26	16	20	1.93
29287683--29287791	55	2.0	55	92	0	182	37	19	4	38	1.72
29294165--29294196	16	2.0	16	93	0	55	65	0	6	28	1.16
29295549--29295579	13	2.4	13	94	0	53	19	0	0	80	0.71
29298838--29298870	16	2.1	16	94	0	57	18	9	15	57	1.63
29300619--29300681	26	2.4	26	89	0	99	36	12	12	38	1.82
29304761--29304939	52	3.5	51	86	6	224	28	16	28	26	1.97
29304761--29304939	51	3.5	52	85	6	242	28	16	28	26	1.97
29311376--29311420	13	3.6	12	85	8	63	80	6	2	11	0.99
29311388--29311419	12	2.7	12	100	0	64	81	6	0	12	0.87
29312441--29312482	10	3.7	12	81	18	54	69	2	16	11	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29312525--29312603	12	6.6	12	71	16	56	62	0	24	13	1.32
29312548--29312581	15	2.3	15	89	0	50	67	0	29	2	1.05
29312535--29312587	18	2.8	20	68	26	53	64	0	24	11	1.26
29321223--29321375	25	6.1	25	78	8	150	33	20	18	26	1.96
29324205--29324277	26	2.8	26	82	10	78	42	6	15	35	1.73
29326633--29326673	21	2.0	21	85	9	57	36	4	4	53	1.44
29326633--29326674	22	2.0	21	81	13	50	38	4	4	52	1.44
29329501--29329571	20	3.5	20	68	0	61	14	29	21	35	1.92
29336000--29336158	45	3.6	45	83	5	164	22	13	28	35	1.92
29346295--29346354	29	2.1	29	100	0	120	48	20	10	21	1.78
29354234--29354678	138	3.2	138	90	0	701	44	6	8	40	1.61
29354568--29354792	118	1.9	118	90	3	364	44	7	7	40	1.60
29354423--29354912	256	1.9	256	91	0	793	44	6	8	41	1.60
29356128--29356318	41	4.7	41	82	4	228	20	20	28	29	1.98
29356150--29356318	80	2.1	80	84	5	216	19	22	28	28	1.98
29356321--29356354	18	1.9	17	88	5	50	23	2	8	64	1.36
29356403--29356457	25	2.2	26	78	9	62	61	7	9	21	1.50
29356667--29356718	15	3.5	15	84	5	61	30	0	36	32	1.58
29356684--29356791	14	7.6	14	73	10	67	25	0	39	35	1.56
29356684--29356759	7	10.9	7	78	10	75	23	0	43	32	1.54
29356698--29356788	35	2.6	35	79	8	96	24	0	41	34	1.55
29356829--29356876	25	1.9	25	95	0	87	35	0	2	62	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29357074--29357111	7	5.4	7	81	12	51	15	2	50	31	1.58
29357074--29357118	14	3.2	14	78	12	56	20	2	46	31	1.62
29356508--29357204	341	2.0	342	82	7	840	31	2	22	43	1.68
29359458--29359499	22	1.9	21	85	9	57	54	11	0	33	1.37
29361543--29361853	43	7.3	43	83	2	374	28	16	28	26	1.97
29361543--29361849	128	2.4	129	84	1	393	28	16	28	25	1.97
29367876--29368055	23	8.0	23	82	4	215	17	21	23	37	1.94
29367889--29368054	46	3.7	46	96	2	302	17	20	24	37	1.94
29373178--29373328	41	3.7	41	94	0	268	21	21	27	29	1.99
29373768--29373833	20	3.2	20	77	12	71	16	1	43	37	1.57
29373768--29373831	27	2.3	27	79	15	69	15	1	45	37	1.56
29373768--29373833	7	9.6	7	77	14	66	16	1	43	37	1.57
29378428--29378475	22	2.0	23	84	11	62	54	2	2	41	1.24
29378525--29378638	43	2.7	43	91	1	185	18	18	35	28	1.94
29378651--29378722	31	2.3	31	95	0	126	27	27	26	18	1.98
29378838--29378881	22	2.0	22	90	0	70	43	25	20	11	1.85
29383051--29383285	81	2.9	81	87	2	348	31	10	25	33	1.90
29410284--29410318	12	2.9	12	95	0	61	17	22	8	51	1.72
29410276--29410326	12	4.2	12	82	9	59	19	23	5	50	1.69
29410578--29410799	50	4.3	50	84	3	246	22	29	22	25	1.99
29418718--29418759	21	2.0	21	90	4	68	71	0	2	26	0.98
29418725--29418842	10	12.3	10	66	13	52	64	1	5	28	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29418718--29418835	19	6.2	19	75	10	82	63	1	5	29	1.25
29418736--29418890	37	4.1	38	74	15	119	61	1	6	30	1.32
29418737--29418851	19	6.2	18	74	14	74	61	1	4	32	1.25
29418737--29418842	9	11.4	9	72	15	74	63	1	4	30	1.26
29418737--29418911	38	4.6	36	75	14	124	60	2	6	30	1.34
29419193--29419377	88	2.1	85	83	6	237	32	9	18	38	1.84
29420862--29420923	31	2.0	31	96	0	115	32	11	16	40	1.83
29427048--29427109	31	2.0	31	96	0	115	32	11	16	40	1.83
29434193--29434341	43	3.5	42	78	5	158	23	18	28	29	1.98
29448549--29448622	33	2.2	33	90	0	112	32	12	18	36	1.88
29448867--29448960	40	2.4	41	81	10	108	37	23	19	20	1.94
29448994--29449200	41	5.0	41	90	2	299	22	21	27	28	1.99
29449539--29449586	15	3.3	14	79	5	51	18	2	35	43	1.62
29449539--29449667	7	18.0	7	74	7	89	18	0	39	41	1.56
29449549--29449667	21	5.5	21	75	4	103	18	0	39	41	1.56
29449539--29449666	29	4.5	28	73	11	98	18	0	39	41	1.56
29449818--29449850	14	2.3	15	89	5	50	15	0	45	39	1.46
29449811--29449903	22	4.2	22	76	11	73	19	1	41	37	1.59
29449821--29449894	39	1.9	38	86	2	103	20	1	41	36	1.61
29450656--29450781	40	3.2	40	68	13	125	18	37	3	40	1.69
29450655--29450806	78	1.9	78	96	2	279	19	38	4	37	1.72
29451337--29451642	43	7.2	43	82	4	350	27	29	18	23	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29451337--29451642	85	3.6	85	82	3	348	27	29	18	23	1.98
29451337--29451642	128	2.4	128	84	4	359	27	29	18	23	1.98
29451660--29451686	14	1.9	14	100	0	54	44	3	0	51	1.19
29453012--29453276	114	2.3	113	83	1	307	27	21	23	27	1.99
29453683--29453736	15	3.5	15	84	5	63	16	0	50	33	1.46
29465647--29465708	27	2.2	27	80	5	70	53	1	9	35	1.44
29465908--29465941	3	11.3	3	100	0	68	67	0	0	32	0.91
29468159--29469460	100	13.2	100	80	5	1025	23	20	23	32	1.98
29468159--29469175	498	2.0	499	84	3	1321	23	20	23	32	1.98
29468293--29469168	50	17.6	49	66	12	318	22	20	24	32	1.98
29469136--29469462	95	3.4	95	89	0	458	25	21	21	31	1.98
29469185--29469450	50	5.5	50	75	9	266	25	22	21	30	1.99
29470809--29470851	8	5.4	8	81	10	52	11	11	0	76	1.02
29470815--29470865	21	2.3	22	86	10	68	15	13	0	70	1.17
29470818--29470854	16	2.5	15	87	12	58	16	13	0	70	1.17
29471664--29471692	6	5.0	6	91	8	51	0	17	0	82	0.66
29471664--29471692	11	2.5	12	94	5	51	0	17	0	82	0.66
29471702--29471763	9	7.0	9	82	10	83	11	0	4	83	0.78
29471688--29471762	25	2.9	26	82	9	82	10	1	6	81	0.93
29471698--29471765	19	3.8	19	81	11	90	11	0	5	82	0.83
29471677--29471763	44	2.0	43	81	6	102	9	3	5	81	0.96
29472998--29473038	19	2.2	19	86	8	57	41	7	19	31	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29474672--29474699	3	9.3	3	100	0	56	67	0	0	32	0.91
29475972--29476052	5	16.6	5	71	21	57	38	3	1	56	1.25
29476084--29476150	35	1.9	34	85	8	91	67	2	23	5	1.27
29483750--29483834	20	4.2	20	84	0	116	38	22	28	10	1.87
29483815--29483945	22	6.0	22	70	17	85	45	13	22	17	1.84
29483852--29483939	44	2.0	44	84	8	117	45	11	23	19	1.83
29485095--29485139	23	2.0	23	82	8	56	28	20	8	42	1.82
29496202--29496272	22	3.3	20	72	16	61	46	15	12	25	1.81
29496177--29496303	44	2.8	45	83	5	152	42	16	15	25	1.87
29504622--29504651	7	4.1	7	95	4	51	60	0	0	40	0.97

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