genome.fa.s1.2.7.7.80.10.50.1000.144.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  144  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)
42993769--42993816	20	2.5	19	83	9	62	56	0	4	39	1.19
42996571--42996621	22	2.3	23	86	6	77	33	19	15	31	1.93
43002886--43002936	12	4.3	12	80	2	50	70	1	13	13	1.25
43003123--43003201	6	12.7	6	76	16	72	74	3	2	18	1.08
43003123--43003201	20	4.2	19	74	20	69	74	3	2	18	1.08
43006407--43006483	30	2.6	30	78	12	88	55	3	14	25	1.56
43006583--43006621	20	2.0	20	89	0	60	56	5	7	30	1.49
43008001--43008041	19	2.2	19	91	4	66	26	9	12	51	1.70
43009376--43009417	21	2.0	23	86	13	63	35	19	19	26	1.95
43020988--43021040	24	2.3	22	74	6	52	26	3	15	54	1.57
43021021--43021058	19	2.1	18	85	14	51	23	0	10	65	1.23
43021114--43021163	20	2.5	21	81	18	63	12	0	26	62	1.30
43031859--43031926	34	2.0	34	88	0	100	22	17	7	52	1.69
43033916--43033998	38	2.4	32	78	21	112	32	20	13	33	1.91
43059317--43059382	31	2.1	31	85	0	87	48	19	12	19	1.80
43060115--43060154	20	2.0	20	85	0	53	52	2	12	32	1.52
43063664--43063729	31	2.1	31	91	0	105	48	19	10	21	1.79
43066657--43066696	20	2.0	20	85	0	53	52	2	12	32	1.52
43071871--43071936	31	2.1	31	85	0	87	45	19	15	19	1.85
43079018--43079089	36	2.0	36	97	0	135	26	19	16	37	1.93
43088898--43089093	41	4.8	41	83	5	236	15	24	26	34	1.95
43088896--43089093	82	2.4	82	93	0	333	15	25	25	33	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43090321--43090351	2	15.5	2	100	0	62	51	0	0	48	1.00
43090886--43091002	7	15.9	7	72	10	72	22	0	44	32	1.59
43090868--43091002	22	6.1	21	76	13	94	22	0	44	32	1.58
43090865--43091003	7	19.0	7	70	16	68	22	0	43	33	1.59
43094667--43094758	13	6.9	13	74	18	91	45	9	1	43	1.44
43094650--43094901	40	6.5	38	79	10	217	44	11	1	42	1.47
43094664--43094767	13	7.8	13	73	16	79	44	11	1	42	1.51
43094799--43094889	18	4.9	18	74	15	87	45	12	0	42	1.41
43094790--43094893	22	5.1	22	69	25	77	43	12	0	44	1.42
43094799--43094860	17	3.6	17	84	4	70	45	12	0	41	1.42
43095166--43095204	20	2.0	19	95	5	69	53	15	0	30	1.42
43095165--43095385	25	9.3	24	71	17	119	47	21	1	30	1.59
43095211--43095385	34	4.7	35	70	21	131	46	21	1	30	1.58
43095185--43095381	59	3.3	59	80	5	272	47	21	1	29	1.60
43095233--43095546	84	3.7	84	73	16	297	44	20	3	31	1.69
43095168--43095416	118	2.1	119	90	7	391	46	20	2	30	1.65
43095375--43095460	25	3.4	25	72	12	95	40	16	9	33	1.80
43095351--43095466	50	2.3	50	95	0	214	43	16	6	32	1.74
43095233--43095541	168	1.8	166	91	4	505	44	20	3	31	1.69
43095484--43095546	25	2.5	25	86	0	90	44	23	3	28	1.69
43100080--43100225	43	3.4	42	84	8	161	24	23	19	31	1.98
43100594--43100628	3	11.7	3	100	0	70	65	0	0	34	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43101956--43101990	14	2.4	15	90	4	54	5	0	20	74	1.02
43104273--43104311	4	9.8	4	94	0	69	48	23	2	25	1.63
43107372--43107413	22	2.0	22	85	4	59	50	19	9	21	1.75
43108468--43108511	6	7.3	6	82	10	54	29	6	47	15	1.72
43114289--43114334	12	3.8	12	85	0	56	21	13	15	50	1.78
43118684--43118747	22	2.9	22	77	11	67	62	3	1	32	1.20
43126604--43126635	6	5.5	6	96	3	57	71	12	0	15	1.14
43139180--43139317	37	3.7	37	83	0	168	16	14	26	42	1.87
43143583--43143616	17	2.0	18	88	11	54	47	0	11	41	1.40
43144749--43144784	19	1.9	18	88	5	54	58	0	0	41	0.98
43152586--43152634	21	2.5	19	80	9	55	61	10	4	24	1.45
43153252--43153290	17	2.3	17	95	0	69	15	43	25	15	1.86
43158081--43158129	22	2.2	22	88	0	71	34	18	16	30	1.93
43159783--43159843	30	2.0	30	90	6	97	24	16	24	34	1.95
43162134--43162172	18	2.2	17	86	13	53	33	0	20	46	1.51
43162386--43162489	23	4.5	23	95	0	172	20	24	25	30	1.98
43164137--43164191	26	2.1	26	86	0	74	29	20	9	41	1.82
43164151--43164210	26	2.3	27	82	5	79	26	16	13	43	1.85
43171624--43171683	30	2.0	31	86	3	86	38	1	40	20	1.62
43171819--43171859	21	2.0	21	85	9	57	43	0	34	21	1.53
43171889--43171925	9	4.1	9	92	0	65	29	10	13	45	1.77
43176765--43176850	42	2.0	42	100	0	172	44	16	20	18	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43186404--43186446	20	2.1	20	83	12	52	51	6	6	34	1.56
43186819--43186852	16	2.1	16	88	5	50	41	8	0	50	1.34
43187895--43187953	31	1.9	31	100	0	118	18	22	11	47	1.81
43193120--43193193	29	2.5	29	82	4	85	25	14	13	45	1.82
43195578--43195626	7	7.0	7	78	17	57	30	14	2	53	1.52
43195578--43195634	21	2.8	20	83	5	69	29	17	1	50	1.56
43195578--43195632	14	3.9	15	79	13	62	30	18	1	49	1.58
43195784--43195830	24	2.0	24	83	8	60	29	0	10	59	1.31
43197120--43197162	18	2.2	20	88	8	63	23	2	2	72	1.08
43205294--43207245	69	28.3	69	67	8	442	31	25	15	27	1.96
43205291--43207266	138	14.3	138	76	4	1316	31	25	15	27	1.96
43205294--43207267	276	7.2	276	77	4	1507	31	25	15	27	1.96
43210688--43210742	21	2.6	21	88	0	74	20	41	21	16	1.90
43211829--43211871	13	3.3	13	80	0	50	39	20	2	37	1.66
43211764--43211871	53	2.1	52	82	5	128	36	20	2	40	1.67
43220171--43220216	17	2.7	17	90	9	76	13	17	32	36	1.88
43220269--43220329	18	3.4	18	79	2	70	14	16	26	42	1.87
43241545--43241569	12	2.1	12	100	0	50	56	16	0	28	1.41
43243167--43243280	41	2.7	43	83	2	133	26	29	17	26	1.97
43243433--43243871	64	6.9	64	89	1	614	41	14	10	33	1.81
43243433--43243871	32	13.7	32	78	1	405	41	14	10	33	1.81
43246970--43247007	19	2.1	19	90	5	60	36	0	5	57	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43246992--43247027	19	2.0	17	89	10	54	27	0	11	61	1.30
43261887--43261970	43	2.0	43	92	0	141	26	17	25	30	1.97
43262264--43262308	21	2.1	21	84	8	56	0	28	22	48	1.50
43263280--43263348	34	2.0	34	100	0	138	17	20	11	50	1.76
43268073--43268112	3	13.3	3	94	0	71	67	0	2	30	1.04
43268110--43268178	33	2.1	33	86	10	97	50	4	7	37	1.50
43272486--43272515	14	2.1	14	93	0	51	20	13	13	53	1.72
43272546--43272604	30	2.0	30	96	0	109	25	5	15	54	1.61
43272730--43272763	12	3.0	12	87	12	54	64	0	0	35	0.94
43276452--43276496	3	14.3	3	86	9	63	28	2	4	64	1.25
43276641--43276695	24	2.2	24	83	3	74	41	5	1	50	1.36
43283372--43283417	21	2.1	22	88	11	69	30	0	43	26	1.55
43283500--43283558	30	2.0	29	90	3	91	38	0	40	20	1.53
43286053--43286109	29	1.9	30	86	10	82	26	10	7	56	1.59
43288340--43288435	47	2.0	47	93	0	165	46	12	14	26	1.80
43296949--43296983	6	5.8	6	93	0	61	14	31	2	51	1.57
43296950--43296989	12	3.3	12	92	0	62	10	30	5	55	1.54
43309864--43309991	39	3.2	39	78	7	150	42	19	5	32	1.74
43312884--43312927	21	2.1	21	100	0	88	29	13	4	52	1.60
43316200--43316567	102	3.6	102	90	1	585	18	20	29	31	1.96
43316478--43316532	28	2.0	28	92	0	92	14	23	34	27	1.94
43320464--43320489	11	2.4	11	100	0	52	38	7	0	53	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43320486--43320547	9	6.4	10	76	23	53	29	1	0	69	0.98
43320456--43320579	40	3.1	41	85	7	177	33	3	0	62	1.11
43320803--43320874	30	2.5	30	70	4	76	43	4	1	51	1.29
43321461--43321541	35	2.3	36	91	4	137	27	29	25	17	1.97
43322431--43322485	25	2.2	25	77	6	58	34	1	5	58	1.32
43322843--43322898	29	1.9	29	89	7	87	39	7	12	41	1.70
43349439--43349502	28	2.3	28	80	0	74	39	17	10	32	1.84
43354786--43354944	37	4.3	37	81	0	174	35	18	20	24	1.95
43354786--43354944	74	2.1	74	83	0	192	35	18	20	24	1.95
43358762--43358800	9	4.4	9	80	6	53	48	0	2	48	1.15

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