genome.fa.s1.2.7.7.80.10.50.1000.158.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  158  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)
46685333--46685377	23	2.0	23	86	8	65	46	11	6	35	1.66
46689445--46689477	17	2.0	17	88	5	50	30	9	12	48	1.71
46690183--46690268	43	2.0	43	100	0	172	37	13	9	39	1.78
46691399--46691452	26	2.1	25	83	10	65	25	7	1	64	1.30
46705284--46705411	50	2.5	51	85	6	172	28	17	23	29	1.97
46706097--46706128	6	5.2	6	96	3	55	81	0	3	15	0.82
46706702--46706758	21	2.7	21	94	0	105	36	10	10	42	1.74
46706987--46707931	132	7.2	132	90	1	1448	25	23	20	30	1.98
46707037--46707881	44	19.2	44	63	13	166	25	23	19	31	1.98
46709168--46709195	6	4.7	6	100	0	56	0	14	0	85	0.59
46709178--46709219	22	1.9	22	90	9	68	7	16	0	76	1.00
46712733--46712795	23	2.6	23	78	16	65	60	4	1	33	1.27
46713278--46713323	22	2.1	22	100	0	92	8	17	4	69	1.31
46713431--46713523	21	4.4	21	81	8	93	40	12	6	39	1.69
46713733--46713817	44	1.9	44	85	4	118	28	24	17	29	1.97
46714077--46714519	132	3.4	132	93	0	742	25	23	20	30	1.99
46714158--46714516	44	8.2	44	64	11	117	26	22	20	30	1.98
46714470--46714747	88	3.1	87	85	4	360	23	23	25	28	1.99
46714554--46714692	44	3.2	43	64	11	102	25	25	23	24	2.00
46722091--46722198	23	4.8	23	69	20	68	57	5	3	33	1.40
46722774--46722830	21	2.7	21	94	0	105	36	10	10	42	1.74
46723860--46723907	8	5.9	8	82	4	60	16	4	0	79	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46723862--46723905	17	2.5	17	88	3	61	15	4	0	79	0.89
46743375--46743421	11	4.6	10	80	12	51	31	4	2	61	1.27
46743414--46743480	19	3.2	20	79	16	75	40	0	4	55	1.20
46743918--46743979	13	4.5	13	74	20	54	59	0	3	37	1.13
46743913--46743995	31	2.6	32	81	12	109	61	0	2	36	1.09
46743931--46743966	18	2.0	18	100	0	72	61	0	5	33	1.19
46745187--46745244	29	1.9	31	86	6	84	20	12	3	63	1.42
46745335--46745375	21	2.0	21	85	0	55	60	2	0	36	1.10
46746913--46746968	21	2.7	21	72	10	60	55	5	1	37	1.33
46749860--46749992	54	2.5	54	89	0	194	14	29	24	31	1.94
46751212--46751264	26	2.0	26	100	0	106	62	11	15	11	1.55
46752157--46752213	26	2.2	27	87	9	91	61	14	15	8	1.56
46752166--46752218	26	2.0	26	100	0	106	62	11	15	11	1.55
46751149--46753060	954	2.0	954	93	0	3304	28	23	14	33	1.94
46759825--46759870	24	1.9	24	81	0	56	34	0	4	60	1.16
46783370--46783428	19	3.0	19	80	9	57	52	5	1	40	1.33
46783377--46783428	19	2.6	21	80	17	58	55	3	1	38	1.29
46783573--46783605	3	11.0	3	100	0	66	33	0	0	66	0.92
46792378--46792416	18	2.1	19	85	4	53	43	15	12	28	1.83
46807185--46807267	32	2.6	32	86	0	112	28	2	18	50	1.59
46808594--46808633	14	2.7	15	84	7	55	52	0	0	47	1.00
46808912--46808938	6	4.5	6	100	0	54	0	37	14	48	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46810795--46810825	16	1.9	16	93	0	53	48	9	6	35	1.62
46810982--46811066	18	4.8	17	72	12	55	34	0	9	56	1.32
46812043--46812071	2	14.5	2	100	0	58	0	48	0	51	1.00
46815384--46815432	24	2.0	24	100	0	98	38	12	8	40	1.72
46821448--46821473	3	8.7	3	100	0	52	34	65	0	0	0.93
46832279--46832389	46	2.4	46	95	1	197	29	21	17	31	1.96
46832266--46832499	37	5.6	45	84	11	243	28	21	14	35	1.93
46836035--46836301	51	5.3	51	92	0	437	29	23	14	33	1.94
46836749--46836811	31	2.0	31	100	0	126	39	15	6	38	1.73
46841784--46841829	24	1.9	25	91	8	78	36	0	2	60	1.09
46842020--46842061	16	2.6	16	92	0	66	42	7	2	47	1.43
46842035--46842096	22	2.8	22	85	0	79	46	1	1	50	1.20
46845807--46845854	25	1.9	25	83	8	62	70	0	10	18	1.15
46847351--46847441	23	4.0	23	92	0	146	21	20	27	29	1.98
46849180--46849317	73	1.9	71	92	2	231	48	13	7	30	1.70
46863840--46864222	211	1.8	211	97	0	730	33	15	9	41	1.79
46871215--46871321	41	2.6	41	94	5	191	65	0	1	32	1.04
46871278--46871338	29	2.1	29	96	3	115	70	0	0	29	0.88
46871209--46871292	12	7.9	11	67	21	54	60	0	2	36	1.10
46871278--46871349	28	2.5	29	90	2	92	68	0	2	29	1.04
46871255--46871351	29	3.2	29	82	7	88	67	0	3	29	1.06
46871306--46871372	20	3.4	20	73	15	68	64	0	2	32	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46871679--46871729	23	2.2	24	85	3	68	7	5	17	68	1.34
46871679--46871729	12	4.3	12	75	5	50	7	5	17	68	1.34
46871689--46871747	24	2.5	24	83	2	66	6	10	18	64	1.46
46874490--46874533	18	2.4	18	84	0	52	70	4	2	22	1.17
46874490--46874541	20	2.7	19	76	11	52	69	3	1	25	1.16
46875287--46875344	18	3.2	18	73	9	64	36	5	1	56	1.32
46875356--46875399	22	2.0	22	86	4	61	25	4	2	68	1.20
46875408--46875471	17	3.5	17	81	14	58	29	6	0	64	1.18
46875422--46875473	20	2.8	18	85	11	61	30	3	0	65	1.10
46875421--46875499	19	4.2	18	79	10	72	27	3	2	65	1.22
46879285--46879370	45	2.0	45	81	4	104	51	8	3	37	1.49
46893835--46893966	50	2.6	52	78	8	146	37	12	15	34	1.85
46896953--46897517	283	2.0	282	99	0	1112	42	7	18	31	1.78
46899628--46899673	20	2.3	20	77	7	58	52	0	0	47	1.00
46900472--46900514	22	2.0	22	85	0	59	23	13	6	55	1.62
46912765--46912937	45	3.8	45	83	3	188	40	16	20	22	1.91
46912860--46912985	45	2.8	45	86	0	171	35	17	21	25	1.95
46912909--46913024	45	2.6	45	78	0	106	39	17	19	23	1.92
46927533--46927572	20	2.0	21	85	5	55	25	7	7	60	1.50
46936740--46936797	28	2.1	28	96	0	107	44	20	17	17	1.86
46941400--46941444	7	6.6	7	87	5	65	55	4	0	40	1.20
46949005--46949041	11	3.2	12	85	7	51	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46950400--46950455	28	2.0	28	93	3	96	71	8	5	14	1.29
46954401--46954502	48	2.1	48	88	0	150	33	7	10	48	1.67
46959895--46959940	2	23.0	2	100	0	92	50	0	0	50	1.00
46974246--46974276	15	2.1	15	100	0	62	32	16	19	32	1.94
46975688--46975728	15	2.5	17	80	11	50	41	0	0	58	0.98
46978877--46978905	13	2.1	14	93	6	51	58	0	6	34	1.25
46984408--46984491	42	2.0	42	97	0	159	36	13	21	28	1.91
46989702--46989749	6	7.7	6	78	17	53	2	20	0	77	0.88
46991582--46991775	105	1.9	101	86	4	271	32	15	23	27	1.95
46991611--46991807	105	1.9	105	83	2	261	34	16	23	25	1.96
46992568--46992725	72	2.2	72	90	0	244	21	29	22	26	1.99
46997021--46997119	51	1.9	51	89	0	153	35	24	8	32	1.85
46997302--46997364	33	1.9	33	86	0	90	22	49	3	25	1.65
46997975--46998185	117	1.8	117	89	0	332	44	24	9	21	1.82
46998372--46998416	16	2.8	16	82	3	54	35	0	22	42	1.54
47010136--47010194	22	2.6	22	76	10	57	28	0	5	66	1.13
47012166--47012338	45	3.9	45	80	3	172	26	13	24	35	1.93
47012164--47012336	90	1.9	88	82	4	213	26	13	24	35	1.92
47018170--47018203	15	2.3	15	94	0	59	20	14	14	50	1.78
47018604--47018647	19	2.4	18	85	7	54	63	2	0	34	1.07
47019133--47019162	14	2.1	14	93	0	51	30	0	0	70	0.88
47019180--47019236	29	1.9	29	85	3	78	52	3	1	42	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47027730--47028110	190	2.0	190	96	0	708	34	22	17	25	1.96
47029441--47029522	26	3.4	23	76	15	76	64	8	1	25	1.29
47029455--47029521	26	2.7	26	79	6	77	65	10	0	23	1.23
47031152--47031216	14	4.8	13	73	17	53	44	3	0	52	1.16
47035039--47035193	42	3.7	42	79	5	143	45	15	22	16	1.85
47035094--47035193	21	4.8	21	67	7	60	49	16	21	14	1.80
47035251--47035314	24	2.7	24	95	0	110	21	28	7	42	1.81
47037215--47037271	11	5.1	11	73	12	53	70	5	0	24	1.08
47037215--47037271	21	2.5	23	75	10	64	70	5	0	24	1.08
47039604--47039639	18	2.0	18	100	0	72	38	16	5	38	1.72

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