genome.fa.s8.2.7.7.80.10.50.1000.13.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   

This is table  13  of  190  ( 22705 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)
3888609--3888665	6	9.0	6	88	7	78	35	0	47	17	1.48
3888612--3888665	13	4.2	13	86	9	74	33	0	50	16	1.46
3888609--3888665	19	2.9	19	92	2	87	35	0	47	17	1.48
3888762--3888962	30	6.7	30	85	7	275	51	0	10	37	1.40
3888762--3888962	61	3.4	61	85	6	286	51	0	10	37	1.40
3888866--3888918	26	2.2	23	84	15	79	43	0	11	45	1.40
3892527--3892568	22	2.0	22	85	4	59	66	2	0	30	1.04
3892810--3892862	21	2.5	21	93	0	88	30	39	9	20	1.84
3895653--3895702	10	4.9	10	81	11	57	54	4	0	42	1.19
3895660--3895747	31	2.7	31	76	10	88	57	2	0	39	1.11
3895714--3895825	19	5.9	18	73	17	77	58	1	7	32	1.35
3895831--3895874	22	2.1	20	87	8	61	50	2	2	45	1.27
3895837--3895881	22	2.1	22	88	8	67	60	2	2	35	1.22
3896216--3896319	9	10.5	10	68	16	56	32	3	0	62	1.20
3901944--3901992	3	16.3	3	91	0	80	63	0	4	32	1.13
3909982--3910031	13	3.8	13	79	7	57	32	2	28	38	1.68
3910200--3910261	30	2.1	30	84	6	81	48	0	3	48	1.17
3911887--3911914	6	4.7	6	100	0	56	14	0	50	35	1.43
3913718--3913761	19	2.5	17	79	13	52	40	0	6	52	1.28
3913723--3913776	19	2.8	20	85	2	74	37	0	5	57	1.22
3913729--3913775	20	2.4	20	89	3	69	40	0	2	57	1.11
3915416--3915451	18	2.0	18	94	0	63	30	16	8	44	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3920325--3920369	23	2.0	22	82	4	54	28	2	20	48	1.61
3920613--3920680	26	2.7	26	79	6	77	17	19	22	41	1.91
3920660--3920801	24	5.9	24	65	17	64	18	26	20	34	1.96
3920722--3920839	48	2.4	49	79	10	134	19	25	20	34	1.96
3921027--3921094	5	13.6	5	100	0	136	39	0	20	39	1.53
3924287--3924332	21	2.0	24	84	12	62	39	8	4	47	1.54
3927566--3927971	27	14.2	28	72	11	153	22	17	5	54	1.63
3927640--3927823	96	1.9	95	83	3	235	22	16	5	55	1.61
3927735--3928019	29	10.2	28	74	7	175	23	16	5	54	1.62
3927735--3927926	57	3.4	56	76	9	153	23	16	4	55	1.60
3927833--3927972	53	2.6	55	80	5	160	23	14	6	55	1.62
3927735--3927972	27	8.6	28	76	6	180	23	15	5	55	1.61
3928890--3928941	26	2.0	26	85	7	70	32	21	19	26	1.97
3932143--3932240	50	1.9	51	83	6	128	40	15	5	38	1.69
3934791--3934836	21	2.2	21	88	0	65	36	21	39	2	1.66
3935299--3935507	42	4.9	42	83	9	221	25	23	20	30	1.99
3935298--3935526	43	5.4	42	82	8	259	25	24	20	29	1.99
3935298--3935509	85	2.5	86	87	4	288	25	24	20	30	1.98
3938996--3939067	35	2.1	35	100	0	144	37	13	8	40	1.75
3944335--3944393	22	2.5	24	76	20	63	50	0	3	45	1.18
3947404--3947435	16	1.9	17	93	6	57	46	3	0	50	1.17
3950730--3950978	120	2.0	123	92	3	414	24	15	22	38	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3954152--3954213	29	2.1	30	82	8	74	50	6	6	37	1.54
3963432--3963478	22	2.2	21	88	3	67	59	14	6	19	1.56
3964976--3965036	24	2.5	24	84	10	72	40	24	18	16	1.90
3965059--3965129	27	2.8	25	72	8	70	30	22	28	18	1.97
3966049--3966101	22	2.4	22	96	0	97	33	13	24	28	1.93
3968819--3968890	29	2.3	31	83	9	85	52	0	1	45	1.09
3968822--3968916	36	2.6	37	73	9	88	52	0	1	46	1.07
3976600--3976691	23	3.9	23	88	7	123	23	26	21	28	1.99
3976938--3976994	25	2.3	25	100	0	114	45	7	12	35	1.69
3978598--3978692	24	4.0	24	91	2	138	48	7	5	38	1.54
3980075--3980269	42	4.3	43	76	17	173	42	26	8	23	1.81
3980094--3980406	96	3.3	96	87	4	451	41	25	6	26	1.79
3980190--3980278	42	2.1	42	87	2	135	43	28	7	20	1.79
3980686--3980721	2	18.5	2	94	5	65	50	0	0	50	1.00
3981984--3982351	122	3.0	124	85	8	505	30	13	22	33	1.93
3985718--3985962	23	10.2	23	71	18	171	26	2	23	47	1.63
3985739--3985896	50	3.4	44	81	14	174	29	1	22	46	1.60
3985876--3985942	30	2.2	30	81	0	80	20	2	25	50	1.62
3985968--3986054	44	2.0	45	90	2	140	49	12	0	37	1.41
3987163--3987187	7	3.6	7	100	0	50	60	12	0	28	1.32
3988330--3988443	51	2.3	50	93	1	192	45	0	25	28	1.54
3988417--3988466	22	2.3	22	96	3	93	38	0	34	28	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3989353--3989413	7	8.4	7	80	18	63	70	9	18	1	1.23
3990102--3990128	12	2.2	12	100	0	54	0	62	0	37	0.95
3990191--3990240	25	2.0	25	88	0	73	4	34	4	58	1.36
3991322--3991346	5	5.0	5	100	0	50	80	0	20	0	0.72
3991867--3991905	19	2.1	19	100	0	78	20	10	38	30	1.86
3993212--3993266	21	2.6	21	88	8	85	27	36	9	27	1.87
3993578--3993832	44	5.9	44	87	7	353	21	22	14	42	1.88
3993578--3993814	86	2.8	86	94	1	395	21	21	14	42	1.88
3993578--3993832	130	2.0	129	88	4	379	21	22	14	42	1.88
4002212--4002265	8	6.9	8	74	19	51	51	0	1	46	1.11
4003292--4003431	40	3.5	40	72	12	119	28	18	24	28	1.98
4004440--4004491	2	26.0	2	100	0	104	50	0	0	50	1.00
4005320--4005349	14	2.1	15	93	6	53	40	10	0	50	1.36
4005809--4005870	31	2.0	32	87	3	90	29	16	27	27	1.97
4006214--4006265	27	1.9	27	96	0	95	30	21	13	34	1.92
4008765--4008790	11	2.4	11	100	0	52	38	0	19	42	1.51
4009137--4009214	33	2.3	35	78	10	90	39	0	1	58	1.06
4024391--4024441	19	2.7	19	79	11	61	37	3	3	54	1.37
4035564--4035611	24	2.0	24	100	0	96	54	16	0	29	1.43
4039157--4039189	2	16.5	2	100	0	66	51	0	0	48	1.00
4048780--4048805	13	2.0	13	100	0	52	53	23	0	23	1.46
4048875--4048915	13	3.2	13	76	16	50	46	12	0	41	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4050415--4050483	10	6.6	10	75	21	54	1	17	5	75	1.07
4055839--4055889	10	4.8	10	79	11	57	5	11	1	80	0.97
4055839--4055889	22	2.4	21	77	6	57	5	11	1	80	0.97
4055985--4056014	10	3.0	10	90	0	51	86	0	10	3	0.67
4058039--4058079	17	2.3	18	95	4	75	39	0	14	46	1.45
4061959--4061997	20	2.0	20	85	10	53	46	2	5	46	1.38
4066181--4066328	37	4.0	37	95	0	260	39	13	19	27	1.89
4070850--4070911	25	2.5	25	79	10	65	30	3	3	62	1.26
4076876--4076979	52	2.0	52	98	0	199	32	16	21	29	1.95
4079071--4079096	3	8.7	3	100	0	52	30	0	0	69	0.89
4091826--4092084	44	5.8	44	77	1	257	32	15	23	28	1.95
4091778--4092069	44	6.5	45	76	6	252	32	16	22	28	1.95
4091865--4092084	89	2.5	89	89	0	323	32	16	22	28	1.95
4091778--4092069	133	2.2	135	87	3	408	32	16	22	28	1.95
4093624--4093672	13	3.7	13	80	2	53	24	4	0	71	1.03
4093606--4093672	27	2.6	27	79	15	70	25	4	2	67	1.24
4093603--4093672	37	1.9	36	82	8	88	24	4	2	68	1.21
4093840--4093885	19	2.4	19	100	0	92	30	4	4	60	1.35
4093897--4093930	2	17.0	2	93	0	59	50	2	0	47	1.16
4100440--4100697	98	2.6	99	82	10	287	46	15	6	31	1.72
4102259--4102537	123	2.3	124	94	1	499	30	16	21	32	1.95
4105673--4105760	27	3.2	26	63	12	68	47	12	7	31	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4105772--4106218	30	14.7	30	85	7	591	28	1	24	45	1.60
4105770--4106164	59	6.6	59	88	5	594	28	1	25	45	1.61
4105772--4106218	89	4.9	89	87	6	603	28	1	24	45	1.60
4105793--4106187	184	2.1	184	92	2	650	28	1	25	45	1.62
4106162--4106214	28	2.0	28	85	10	76	24	0	28	47	1.52
4115252--4115307	25	2.3	25	80	14	64	62	5	0	32	1.18
4115404--4115463	10	5.8	10	76	7	57	61	0	0	38	0.96
4115398--4115462	31	2.1	31	97	0	121	64	0	0	35	0.94
4115405--4115462	11	5.5	11	75	4	57	63	0	0	36	0.94
4115497--4115547	22	2.3	21	87	9	75	33	1	35	29	1.69

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