genome.fa.s1.2.7.7.80.10.50.1000.59.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  59  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)
17352361--17352444	43	2.0	43	85	4	116	54	13	13	19	1.70
17369083--17369123	6	6.3	6	84	15	55	78	2	2	17	0.98
17369082--17369129	15	3.4	14	80	16	55	75	2	2	20	1.02
17369221--17369260	7	5.7	7	100	0	80	12	30	15	42	1.83
17373462--17373509	3	16.3	3	89	4	71	62	0	37	0	0.95
17374100--17374190	11	8.9	11	70	22	65	58	0	2	39	1.10
17374106--17374199	30	3.2	30	86	7	122	62	0	2	35	1.07
17374085--17374200	40	2.9	40	83	10	123	61	0	3	35	1.13
17374394--17374466	36	2.0	36	94	0	128	19	10	24	45	1.82
17388118--17388213	37	2.6	37	77	8	97	32	21	3	42	1.69
17388987--17389031	22	2.0	23	87	12	67	66	2	0	31	1.04
17389421--17389469	25	2.0	25	88	8	73	51	6	0	42	1.27
17391944--17391978	18	1.9	18	88	0	52	57	14	8	20	1.63
17391963--17392074	48	2.3	48	100	0	224	54	12	8	24	1.66
17392005--17392098	6	14.7	6	71	12	62	57	11	7	23	1.59
17392053--17392104	18	2.9	18	85	0	68	61	9	5	23	1.48
17395066--17395103	17	2.2	17	95	0	67	47	13	10	28	1.76
17395066--17395112	17	2.8	17	87	6	51	48	14	8	27	1.73
17396080--17396139	12	4.9	12	87	2	84	58	0	26	15	1.37
17396082--17396139	6	9.5	6	86	1	62	58	0	25	15	1.37
17396082--17396139	18	3.2	18	82	2	71	58	0	25	15	1.37
17408034--17408060	13	2.1	13	100	0	54	74	0	0	25	0.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
17409437--17409537	43	2.4	43	86	5	134	21	30	10	36	1.88
17420837--17420871	14	2.5	14	90	9	54	37	5	8	48	1.58
17433504--17433572	34	2.1	34	83	2	86	42	15	8	33	1.78
17435979--17436101	61	2.0	61	100	0	246	29	22	17	30	1.97
17436168--17436218	9	6.2	9	82	13	58	13	0	33	52	1.41
17436163--17436192	15	2.0	15	93	0	51	13	0	36	50	1.42
17436335--17436779	126	3.5	126	86	3	601	31	16	22	28	1.96
17439813--17439960	22	6.6	21	70	18	111	25	0	31	42	1.60
17439886--17439987	49	2.1	48	82	8	118	28	0	25	45	1.60
17439951--17440002	20	2.5	20	81	3	59	23	1	30	44	1.64
17441417--17441454	20	1.9	20	84	10	51	55	7	2	34	1.43
17442415--17442442	11	2.5	11	100	0	56	42	7	28	21	1.79
17442453--17442486	11	2.9	12	86	8	52	41	2	32	23	1.69
17443314--17443360	24	2.0	23	83	4	58	36	0	10	53	1.36
17444421--17444479	24	2.5	23	88	2	82	57	0	1	40	1.09
17448868--17448905	18	2.1	19	85	5	51	31	0	10	57	1.32
17450870--17450986	40	2.9	41	76	2	128	35	14	25	24	1.94
17452665--17452707	20	2.2	20	91	0	68	27	13	11	46	1.78
17453365--17453426	26	2.4	26	83	5	72	40	19	20	19	1.92
17453604--17453666	27	2.3	27	86	0	81	20	15	23	39	1.91
17453615--17453994	27	14.0	27	79	3	300	20	16	18	44	1.86
17453634--17453993	81	4.4	81	79	5	363	20	16	18	45	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
17453931--17454002	27	2.7	26	85	6	99	18	18	22	41	1.90
17458639--17458723	25	3.4	25	78	3	73	32	18	24	23	1.97
17458676--17458725	25	2.0	25	92	0	82	30	14	30	26	1.94
17458684--17458773	25	3.6	25	80	8	87	35	15	26	22	1.94
17458759--17458880	25	4.9	24	75	14	97	38	19	22	18	1.93
17463465--17463503	18	2.2	18	100	0	78	20	15	33	30	1.94
17466689--17466734	22	2.1	22	84	8	58	41	6	13	39	1.70
17469745--17469785	16	2.4	18	80	12	50	41	7	0	51	1.30
17472825--17472964	72	1.9	72	83	0	181	44	16	13	25	1.84
17474752--17474785	18	2.0	18	88	11	54	58	5	5	29	1.45
17475407--17475458	25	2.2	23	83	13	61	61	3	0	34	1.14
17475441--17475470	13	2.3	13	94	0	51	73	0	3	23	0.98
17475689--17475745	7	8.0	7	74	18	55	71	3	0	24	1.01
17475705--17475744	21	1.9	21	94	0	71	75	5	0	20	0.99
17476937--17476967	9	3.4	9	90	0	53	38	22	12	25	1.90
17477329--17477419	41	2.2	41	100	0	182	24	27	27	20	1.99
17477608--17477641	11	3.0	11	91	4	50	20	32	0	47	1.51
17477623--17477657	18	1.9	18	94	0	61	22	28	2	45	1.67
17477619--17477699	29	2.7	30	74	14	87	24	29	1	44	1.62
17478856--17478898	7	6.1	7	100	0	86	27	0	13	58	1.37
17479546--17479589	18	2.4	18	80	0	52	18	25	6	50	1.71
17479844--17479890	21	2.2	21	84	0	58	27	44	23	4	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
17481348--17481376	15	1.9	15	100	0	58	48	37	0	13	1.43
17481900--17481931	16	2.0	16	93	0	55	46	0	0	53	1.00
17482010--17482048	19	2.1	19	90	0	60	48	7	7	35	1.61
17484842--17484911	3	23.3	3	76	5	70	30	5	1	62	1.27
17484940--17484984	23	1.9	24	81	4	56	33	2	6	57	1.37
17492587--17492611	13	1.9	13	100	0	50	28	0	0	72	0.86
17495809--17495863	3	18.3	3	100	0	110	32	0	0	67	0.91
17502000--17502040	2	21.0	2	95	5	75	48	0	0	51	1.00
17502403--17502441	14	2.8	14	84	0	51	33	2	7	56	1.41
17508101--17508137	19	2.1	17	90	10	56	37	0	2	59	1.12
17511137--17511181	22	2.0	22	95	0	81	46	20	8	24	1.78
17515776--17515820	22	2.0	22	95	0	81	46	20	8	24	1.78
17529617--17529643	14	1.9	14	100	0	54	29	14	14	40	1.86
17533112--17533140	6	4.8	6	100	0	58	34	0	48	17	1.47
17535455--17535642	94	2.0	92	92	2	313	27	22	13	36	1.91
17536189--17536228	20	2.0	20	100	0	80	30	30	10	30	1.90
17540632--17540710	9	9.8	9	66	27	52	69	1	2	26	1.09
17540639--17540709	24	3.1	22	78	9	63	70	1	2	25	1.09
17540639--17540709	16	4.6	14	77	17	70	70	1	2	25	1.09
17540620--17540710	16	5.6	16	73	12	69	67	2	2	28	1.15
17546995--17547040	16	2.8	17	78	12	51	54	2	4	39	1.32
17547848--17547881	17	1.9	18	88	5	52	79	0	5	14	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
17556257--17556380	62	2.0	62	87	3	178	36	7	25	31	1.83
17559266--17559428	50	3.3	49	74	3	164	23	25	20	30	1.98
17559282--17559481	100	2.0	99	87	4	287	23	24	22	30	1.99
17567549--17567608	20	3.0	20	97	0	111	28	15	26	30	1.96
17572770--17572812	9	4.8	9	85	0	50	46	0	0	53	1.00
17572815--17572847	3	11.0	3	100	0	66	0	0	33	66	0.92
17573121--17573155	18	1.9	18	88	0	52	40	5	0	54	1.24
17575263--17575321	22	2.6	22	76	10	57	28	0	5	66	1.13
17580970--17581139	43	3.9	44	73	3	146	27	24	24	23	2.00
17581004--17581139	44	3.1	44	74	4	166	26	22	25	25	2.00
17580938--17581205	88	3.0	88	87	1	385	28	24	23	23	1.99
17581172--17581547	44	8.7	44	84	6	439	28	17	26	28	1.98
17581211--17581554	126	2.7	129	90	4	525	28	17	26	27	1.98
17581172--17581501	170	1.9	170	90	2	520	28	17	25	28	1.97
17581854--17582007	44	3.6	43	73	10	129	26	21	22	29	1.99
17583407--17583454	3	16.0	3	100	0	96	0	0	33	66	0.92
17583738--17583772	18	1.9	18	88	0	52	40	5	0	54	1.24
17585255--17585294	17	2.3	18	83	12	57	47	5	7	40	1.54
17587783--17587838	28	2.0	28	100	0	112	21	17	7	53	1.67
17589405--17589435	14	2.2	14	100	0	62	19	22	0	58	1.40
17595483--17595528	7	5.8	8	82	12	51	76	2	0	21	0.90
17595484--17595517	7	4.7	7	96	3	59	76	0	0	23	0.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
17600702--17600733	15	2.1	15	94	5	55	59	6	0	34	1.23
17603298--17603331	16	2.1	17	88	5	52	35	0	0	64	0.94
17607578--17607618	21	2.0	21	90	0	64	26	12	9	51	1.70
17608951--17608988	20	2.0	20	89	5	60	28	0	31	39	1.57
17621134--17621199	31	2.1	31	97	0	123	31	19	9	39	1.83
17622546--17622571	8	3.2	8	100	0	52	88	0	0	11	0.52
17628474--17628503	11	2.7	11	100	0	60	36	16	16	30	1.91
17628933--17628967	18	1.9	18	88	0	52	42	17	17	22	1.88
17633417--17633446	14	2.1	14	100	0	60	73	0	6	20	1.05
17633433--17633487	18	3.0	18	81	7	58	70	3	16	9	1.27

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