genome.fa.s8.2.7.7.80.10.50.1000.15.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  15  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)
4382080--4382149	16	4.2	16	74	16	52	38	4	0	57	1.19
4382459--4382599	20	6.8	21	68	16	80	54	2	2	41	1.24
4382436--4382497	29	2.2	28	83	16	83	62	0	0	37	0.95
4382524--4382590	20	3.1	21	85	8	82	53	1	0	44	1.09
4382554--4382618	31	2.1	32	88	8	98	60	1	1	36	1.16
4382577--4382601	11	2.3	11	100	0	50	64	0	0	36	0.94
4382662--4382705	9	4.9	9	83	10	54	75	4	0	20	0.98
4382720--4382783	19	3.3	19	76	12	67	73	3	6	17	1.17
4382674--4382794	17	7.5	15	67	18	57	75	2	4	17	1.09
4383804--4383858	7	7.4	7	79	18	58	69	10	18	1	1.27
4384473--4384506	17	1.9	18	94	5	61	32	35	29	2	1.73
4384911--4384966	27	2.1	27	87	6	80	30	37	10	21	1.87
4387092--4387129	2	19.5	2	94	5	69	50	0	0	50	1.00
4387633--4387670	2	19.0	2	100	0	76	50	0	0	50	1.00
4388181--4388287	41	2.6	41	79	5	101	30	26	16	26	1.97
4388822--4388864	22	2.0	22	100	0	86	23	25	13	37	1.92
4389938--4389962	13	1.9	13	100	0	50	40	24	4	32	1.73
4393238--4393269	2	16.0	2	100	0	64	50	0	0	50	1.00
4395763--4395804	2	21.0	2	100	0	84	50	0	0	50	1.00
4396249--4396275	2	13.5	2	100	0	54	48	0	0	51	1.00
4397351--4397404	26	2.1	26	85	0	72	35	12	25	25	1.92
4397610--4397666	10	5.9	10	78	13	57	29	0	3	66	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4397628--4397655	11	2.5	11	100	0	56	25	0	7	67	1.15
4397661--4397749	20	4.3	20	76	12	74	38	0	5	56	1.23
4404460--4404581	54	2.3	54	78	8	133	22	27	30	20	1.98
4407343--4407389	23	2.0	23	91	0	76	31	14	10	42	1.80
4429196--4429249	24	2.2	24	83	6	65	29	3	29	37	1.75
4434318--4434351	16	2.1	17	88	5	52	67	0	2	29	1.05
4434327--4434377	18	2.9	18	75	11	52	66	0	7	25	1.18
4434505--4434539	17	2.1	17	88	0	52	37	0	0	62	0.95
4434514--4434551	18	2.1	19	85	5	51	31	2	0	65	1.06
4435810--4435843	17	1.9	18	88	5	52	50	0	8	41	1.34
4435982--4436050	26	2.5	27	81	6	77	43	1	14	40	1.54
4436230--4436271	3	14.0	3	100	0	84	66	0	0	33	0.92
4438017--4438076	10	6.3	10	73	22	58	40	1	0	58	1.08
4438033--4438093	19	3.1	19	82	17	72	36	3	0	60	1.13
4440112--4440164	19	2.7	21	77	8	58	45	13	0	41	1.43
4440177--4440228	23	2.3	23	83	6	61	48	9	3	38	1.54
4440327--4440373	22	2.2	21	81	11	51	55	6	0	38	1.26
4440112--4440582	149	3.2	146	85	7	580	46	9	4	39	1.57
4440143--4440583	147	3.0	148	87	5	597	46	9	4	39	1.57
4441303--4441334	16	2.0	16	100	0	64	25	6	25	43	1.77
4442400--4442439	20	2.0	20	85	5	53	42	0	10	47	1.37
4442723--4442776	23	2.3	23	87	3	72	27	27	20	24	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4442982--4443071	24	3.7	24	69	16	69	23	21	16	38	1.92
4449277--4449323	19	2.5	19	86	6	60	2	12	4	80	0.94
4453933--4454017	20	4.2	20	78	14	86	36	0	2	61	1.09
4453934--4454016	38	2.1	40	88	6	125	37	0	2	60	1.10
4454593--4454623	16	1.9	16	93	0	53	29	0	0	70	0.87
4457986--4458061	37	2.1	37	100	0	152	31	7	18	42	1.79
4459540--4459564	13	1.9	13	100	0	50	12	24	32	32	1.91
4460025--4460066	15	2.7	16	82	14	52	45	0	2	52	1.13
4460016--4460057	15	2.9	15	82	10	52	47	0	0	52	1.00
4460169--4460203	18	2.0	17	88	5	52	45	0	0	54	0.99
4460000--4460316	157	2.0	157	96	0	589	47	5	3	44	1.41
4460349--4460458	45	2.6	43	79	11	120	32	29	5	32	1.80
4460439--4460506	16	4.2	16	88	0	100	35	33	0	30	1.58
4460435--4460506	32	2.2	32	95	0	126	34	33	0	31	1.58
4464540--4464608	34	2.0	34	85	0	93	23	15	8	52	1.71
4471096--4471122	3	9.0	3	100	0	54	33	0	0	66	0.92
4489172--4489245	22	3.3	22	64	32	57	47	13	25	13	1.79
4496829--4496864	19	1.9	18	88	5	54	11	33	5	50	1.61
4512012--4512036	4	6.2	4	100	0	50	0	24	0	76	0.80
4513762--4513819	27	2.2	26	84	3	71	32	18	22	25	1.97
4523226--4523801	287	2.0	287	91	1	931	24	14	28	32	1.94
4527466--4527514	25	2.0	24	84	8	62	20	2	2	75	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4528091--4528151	29	2.0	30	87	6	88	45	13	9	31	1.75
4528624--4528779	83	1.9	82	84	5	199	48	7	8	35	1.62
4529213--4529262	26	2.0	25	84	4	64	42	0	6	52	1.26
4530150--4530185	18	1.9	18	88	5	54	25	8	0	66	1.19
4530620--4530676	29	2.0	29	89	6	89	22	40	0	36	1.55
4539501--4539552	21	2.5	21	83	0	68	15	25	19	40	1.90
4541636--4541660	12	2.1	12	100	0	50	24	28	24	24	2.00
4541818--4541898	9	8.9	9	85	8	101	40	29	8	20	1.83
4542044--4542073	13	2.3	13	100	0	60	16	0	43	40	1.48
4546995--4547052	21	2.8	21	81	0	71	20	24	15	39	1.91
4546965--4547067	42	2.5	42	80	0	116	18	22	15	43	1.87
4559515--4559680	90	1.8	90	100	0	332	23	23	10	42	1.85
4560611--4560656	21	2.1	23	84	8	60	39	17	8	34	1.80
4565222--4565274	26	2.0	26	81	7	61	22	11	5	60	1.52
4569185--4569209	10	2.5	10	100	0	50	56	0	8	36	1.29
4569347--4569408	29	2.1	28	85	5	79	24	14	16	45	1.84
4572641--4572682	15	2.6	17	77	14	52	40	0	0	59	0.97
4572825--4572866	20	2.1	20	86	0	57	47	0	7	45	1.30
4574890--4574923	15	2.2	16	89	5	52	41	2	11	44	1.56
4578326--4578365	21	1.9	21	84	0	53	40	17	2	40	1.63
4578679--4578749	26	2.8	26	76	2	81	38	21	21	19	1.94
4580933--4580974	20	2.1	20	90	0	66	50	0	7	42	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4583865--4583927	21	3.0	21	76	0	63	42	20	22	14	1.88
4583859--4584049	42	4.6	42	83	3	206	41	17	21	19	1.90
4583960--4584031	21	3.4	21	69	7	74	40	19	20	19	1.92
4584002--4584071	21	3.4	21	78	7	63	42	15	17	24	1.88
4600015--4600041	2	13.5	2	100	0	54	0	0	48	51	1.00
4600810--4600859	22	2.3	22	89	6	75	34	26	0	40	1.56
4601679--4601716	20	1.9	20	94	0	67	44	26	23	5	1.74
4607914--4607944	12	2.7	11	95	5	53	35	0	0	64	0.94
4611386--4611662	138	2.0	138	91	0	446	45	6	6	41	1.56
4611638--4611789	75	2.0	76	88	2	225	30	13	7	47	1.72
4615833--4615893	29	2.1	29	100	0	122	36	16	11	36	1.85
4620954--4621033	20	4.2	18	80	15	58	62	3	2	31	1.26
4620967--4621043	18	4.1	18	80	14	77	62	2	1	33	1.17
4620932--4621044	19	5.7	19	73	18	65	62	3	2	30	1.25
4629095--4629157	24	2.7	24	85	2	83	25	11	19	44	1.83
4629095--4629164	23	3.0	23	82	2	86	27	10	18	44	1.81
4630000--4630052	24	2.2	24	89	0	79	24	0	5	69	1.09
4630173--4630219	17	2.6	17	86	6	58	29	4	2	63	1.25
4636286--4636323	18	2.1	18	85	9	51	36	2	2	57	1.26
4641279--4641320	3	14.0	3	100	0	84	33	0	0	66	0.92
4642019--4642047	13	2.1	14	93	6	51	41	0	0	58	0.98
4642150--4642229	42	1.9	42	90	10	128	41	5	8	45	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4642326--4642363	2	19.0	2	100	0	76	50	0	0	50	1.00
4642776--4642831	29	1.9	29	85	0	76	28	14	19	37	1.91
4642773--4642836	29	2.2	28	78	5	74	28	15	17	39	1.90
4643107--4643176	22	3.2	21	84	9	86	32	30	0	37	1.58
4643143--4643217	11	7.3	11	72	21	65	32	33	0	34	1.58
4643107--4643217	22	5.2	22	80	13	63	32	31	0	36	1.58
4643148--4643206	30	2.0	30	90	6	93	30	37	0	32	1.58
4643263--4643326	29	2.2	29	83	5	85	40	0	1	57	1.08
4643417--4643450	15	2.3	15	90	5	52	26	0	5	67	1.13
4645596--4645897	23	11.4	28	78	15	259	43	23	1	31	1.62

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