genome.fa.s4.2.7.7.80.10.50.1000.168.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: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

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   188   189   190   191   192   
          193   194   195   196   197   198   

This is table  168  of  198  ( 23681 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)
52834476--52834509	15	2.3	15	89	0	50	67	20	11	0	1.21
52839212--52839250	16	2.6	15	88	8	53	48	5	0	46	1.24
52846889--52846942	12	4.5	12	81	9	65	79	1	18	0	0.82
52846901--52846932	5	6.8	5	86	13	50	84	0	15	0	0.63
52846889--52846940	13	4.2	13	85	4	63	80	1	17	0	0.80
52846889--52846933	18	2.6	17	89	3	63	82	2	15	0	0.77
52850240--52850492	46	5.6	46	95	2	451	28	22	15	32	1.95
52850240--52850492	91	2.8	91	96	1	465	28	22	15	32	1.95
52855352--52855537	37	5.0	37	93	0	300	37	13	20	27	1.91
52855500--52855623	46	2.8	46	90	3	191	32	16	23	27	1.96
52856967--52857309	143	2.4	143	88	0	497	29	19	21	29	1.97
52858414--52858454	22	2.0	22	85	9	59	24	9	0	65	1.22
52858694--52858771	22	3.4	22	72	19	70	16	3	5	74	1.15
52859861--52859900	2	21.0	2	90	10	66	50	0	0	50	1.00
52873667--52873713	17	2.7	18	80	6	62	23	17	34	25	1.96
52882792--52882843	24	2.2	24	85	0	68	50	7	3	38	1.50
52887275--52887326	24	2.2	24	89	0	77	50	9	3	36	1.54
52888095--52888158	27	2.4	27	89	2	94	53	6	1	39	1.36
52896134--52896165	12	2.4	14	85	15	50	43	0	15	40	1.47
52896704--52896763	29	2.1	29	96	0	111	18	13	43	25	1.86
52897576--52897706	42	3.1	42	77	6	106	44	16	21	17	1.87
52897605--52897732	42	3.0	42	80	2	141	42	16	21	19	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
52897658--52897756	21	4.8	21	69	1	56	41	16	21	21	1.90
52900643--52900746	24	4.3	24	72	10	68	18	27	21	32	1.96
52901083--52901107	13	1.9	13	100	0	50	48	20	0	32	1.50
52906821--52906863	21	2.0	21	90	0	68	44	30	2	23	1.66
52906861--52906903	21	2.0	21	90	0	68	27	30	13	27	1.95
52915485--52915604	10	13.1	9	77	11	77	65	0	4	30	1.17
52915511--52915703	20	9.9	19	68	15	92	61	1	4	33	1.24
52915556--52915698	10	14.4	10	71	17	66	62	1	4	32	1.23
52915888--52916006	8	13.3	9	71	18	56	31	1	0	67	1.01
52915942--52916003	8	7.5	8	77	12	63	33	0	0	66	0.92
52915896--52916005	26	3.8	26	65	26	60	30	1	0	67	1.01
52917707--52917765	31	1.9	31	82	0	73	38	5	6	49	1.52
52918117--52918165	14	3.4	14	78	13	55	51	6	8	34	1.57
52928286--52928338	20	2.7	20	78	0	70	32	26	11	30	1.91
52929834--52929910	38	2.0	38	100	0	154	28	20	7	42	1.80
52937509--52937544	18	2.0	18	100	0	72	11	11	0	77	0.99
52939652--52939694	21	2.0	21	86	8	61	34	0	6	58	1.25
52939973--52940037	16	4.1	16	95	0	121	20	35	6	38	1.77
52945764--52945812	25	1.9	26	84	12	66	10	2	22	65	1.34
52947901--52947951	24	2.1	24	96	0	93	21	23	5	49	1.71
52947990--52948141	68	2.2	68	90	0	232	28	26	15	28	1.96
52948996--52949022	12	2.2	12	100	0	54	44	7	0	48	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
52953664--52953820	81	1.9	81	87	5	228	44	22	14	17	1.86
52953648--52953820	27	6.4	27	82	5	199	46	23	13	16	1.83
52954172--52954260	28	3.2	28	85	1	99	28	21	20	30	1.98
52954498--52954534	18	2.1	18	89	0	56	24	2	13	59	1.47
52958697--52958752	21	2.7	21	88	0	85	26	8	35	28	1.87
52962609--52962665	13	4.2	13	78	8	60	22	12	7	57	1.58
52962645--52962727	25	3.4	24	78	9	78	26	14	9	49	1.74
52962609--52962732	12	9.8	12	70	13	70	26	14	8	50	1.70
52966446--52966673	47	4.9	47	92	3	365	28	20	8	42	1.81
52966446--52966678	46	5.0	46	92	2	353	28	20	8	42	1.82
52968398--52968442	22	2.0	22	82	4	54	35	24	6	33	1.82
52970145--52970189	19	2.4	19	85	7	56	24	2	0	73	0.95
52971607--52971706	12	8.0	12	69	11	58	29	12	9	50	1.70
52973613--52973812	39	5.1	39	80	1	204	34	28	18	19	1.95
52979948--52980033	24	3.6	24	82	3	75	12	18	43	25	1.86
52979996--52980058	12	5.2	12	90	0	90	15	19	44	20	1.87
52979978--52980058	36	2.2	36	82	0	90	13	20	41	23	1.88
52979978--52980058	24	3.4	24	85	0	90	13	20	41	23	1.88
52985491--52985552	30	2.1	30	84	6	81	43	4	3	48	1.40
52988287--52988331	3	15.0	3	100	0	90	33	0	33	33	1.58
52988653--52988705	13	4.1	13	87	0	79	26	5	24	43	1.76
53000228--53000333	53	2.0	53	98	0	203	13	19	9	57	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53001726--53001767	22	1.9	22	85	0	57	11	2	23	61	1.42
53011035--53011372	51	6.7	52	80	7	340	29	14	25	30	1.95
53011035--53011376	100	3.4	99	85	4	402	29	14	25	30	1.95
53011030--53011383	151	2.3	152	77	8	398	30	14	24	30	1.95
53013733--53013862	25	5.2	25	70	5	84	20	27	21	30	1.98
53015359--53015559	41	4.9	41	80	10	162	28	11	24	35	1.90
53015359--53015528	41	4.2	41	86	5	202	28	12	24	35	1.91
53023386--53023477	25	3.7	25	85	2	105	18	29	19	32	1.96
53023675--53023724	23	2.2	23	100	0	100	28	10	20	42	1.84
53026577--53026623	2	23.5	2	95	0	85	48	0	2	48	1.13
53027099--53027146	2	24.0	2	95	0	87	47	0	2	50	1.12
53034587--53034766	95	1.9	95	94	0	315	42	12	15	29	1.84
53039427--53039490	31	2.1	31	100	0	128	37	0	9	53	1.34
53049537--53049571	11	3.0	12	91	8	63	74	0	0	25	0.82
53049704--53049764	21	3.1	19	77	11	68	29	3	3	63	1.26
53064464--53064608	41	3.6	40	76	13	129	28	28	19	24	1.98
53065109--53065138	2	15.0	2	100	0	60	50	0	0	50	1.00
53066938--53066971	17	1.9	18	88	5	52	41	8	8	41	1.67
53068544--53068615	27	2.7	26	79	14	74	15	6	38	38	1.74
53071972--53072034	22	2.9	22	92	0	99	34	15	25	23	1.95
53077189--53077227	19	2.1	19	85	9	53	51	0	5	43	1.24
53077335--53077369	2	18.5	2	88	11	56	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)
53080626--53080713	44	2.0	44	100	0	176	34	6	18	40	1.77
53082399--53082452	16	3.4	16	89	0	81	33	1	35	29	1.69
53082431--53082521	44	2.0	44	82	2	110	31	5	27	35	1.80
53082666--53082707	15	2.7	16	85	14	61	50	2	0	47	1.14
53082699--53082999	59	5.0	61	69	15	257	48	6	1	42	1.41
53082669--53082999	120	2.8	120	98	0	635	48	6	1	43	1.40
53082786--53082827	15	2.8	16	85	10	61	50	2	0	47	1.14
53082905--53082956	15	3.6	15	80	12	56	53	1	0	44	1.11
53083125--53083193	26	2.6	25	72	19	68	47	1	2	47	1.25
53083144--53083287	47	3.1	45	67	18	109	49	2	2	45	1.28
53083137--53083279	45	3.2	44	69	17	123	48	2	2	47	1.25
53083103--53083319	91	2.4	91	88	2	319	46	3	3	47	1.36
53086383--53086458	33	2.3	33	97	0	143	35	5	15	43	1.70
53086501--53086583	37	2.2	37	93	0	139	36	8	15	39	1.78
53087820--53087948	69	1.9	69	88	0	195	40	24	9	25	1.85
53088772--53088817	22	2.0	23	83	4	58	60	28	4	6	1.40
53089307--53089414	36	2.9	37	83	4	137	55	12	26	5	1.58
53096337--53096495	79	2.0	79	84	7	207	41	10	16	31	1.82
53098437--53098486	25	2.0	25	84	7	66	70	4	4	22	1.21
53102158--53102209	23	2.3	23	89	0	86	46	11	1	40	1.51
53103255--53103355	31	3.3	30	88	5	123	17	0	44	36	1.56
53103286--53103337	14	3.5	14	80	14	68	17	0	46	36	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53103282--53103334	15	3.5	15	80	14	63	16	0	45	37	1.48
53103983--53104473	109	4.5	109	96	0	869	32	16	12	38	1.86
53104488--53104763	109	2.5	109	94	1	491	33	17	13	36	1.88
53104232--53104731	256	1.9	258	95	1	898	31	16	14	38	1.88
53105243--53105293	26	1.9	27	96	4	95	43	19	25	11	1.85
53107172--53107250	2	39.5	2	100	0	158	0	0	49	50	1.00
53107722--53108048	42	7.7	42	84	9	425	33	21	21	23	1.97
53108426--53108475	21	2.4	21	86	0	73	2	44	18	36	1.61
53113961--53114377	9	47.9	9	67	23	200	32	0	20	46	1.57
53113960--53114045	42	2.0	42	84	6	111	34	2	19	43	1.64

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   188   189   190   191   192   
          193   194   195   196   197   198