genome.fa.s5.2.7.7.80.10.50.1000.13.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: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  64140413

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   199   200   201   202   203   204   205   206   207   208   

This is table  13  of  208  ( 24913 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)
3978945--3978987	22	2.0	22	81	9	52	27	11	4	55	1.55
3982378--3982435	20	2.7	21	76	17	57	37	0	1	60	1.07
3983764--3983797	16	2.1	16	88	0	50	14	5	35	44	1.70
3989373--3989398	5	5.2	5	100	0	52	42	19	19	19	1.90
3990425--3990461	9	4.1	9	92	0	65	29	10	13	45	1.77
3991491--3991548	25	2.4	25	80	13	59	34	5	5	55	1.45
3992977--3993031	28	2.0	28	82	7	67	52	9	3	34	1.50
3993190--3993242	26	2.0	27	88	3	81	47	11	13	28	1.77
3993622--3993654	17	2.0	17	88	5	50	42	18	15	24	1.88
3994237--3994332	50	1.9	50	86	0	138	23	26	19	30	1.98
3994507--3994550	20	2.2	20	92	8	72	27	0	0	72	0.85
3994514--3994566	21	2.5	20	84	9	61	32	0	5	62	1.19
4005226--4005260	17	2.1	17	88	0	52	51	17	5	25	1.67
4008393--4008417	11	2.3	11	100	0	50	56	0	0	44	0.99
4010747--4010789	21	2.0	21	86	0	59	27	2	0	69	1.00
4013914--4013998	40	2.1	39	83	12	102	40	1	0	58	1.05
4026397--4026422	3	8.7	3	100	0	52	0	30	0	69	0.89
4027783--4027847	3	21.3	3	84	3	85	63	0	3	33	1.10
4033062--4033096	3	11.7	3	100	0	70	34	0	0	65	0.93
4033397--4033460	19	3.3	19	70	8	56	34	21	9	34	1.86
4037277--4037304	2	14.0	2	100	0	56	50	0	0	50	1.00
4039727--4039788	29	2.2	29	85	5	83	61	6	6	25	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4044526--4044580	17	3.2	16	75	10	56	65	1	1	30	1.13
4045981--4046034	18	3.2	17	76	5	56	22	0	9	68	1.17
4047857--4047924	9	7.6	9	88	0	100	25	10	25	39	1.87
4047857--4047924	27	2.5	27	95	0	118	25	10	25	39	1.87
4057009--4057059	21	2.5	20	84	9	66	39	5	19	35	1.76
4057723--4057776	27	2.0	26	92	3	90	62	0	1	35	1.06
4060739--4060777	21	2.0	21	90	10	64	41	20	0	38	1.53
4060968--4061012	6	7.5	6	87	0	54	57	4	0	37	1.19
4060968--4061012	18	2.5	18	92	0	72	57	4	0	37	1.19
4060972--4061012	12	3.4	12	93	0	64	56	4	0	39	1.21
4061898--4061924	2	13.5	2	100	0	54	51	0	0	48	1.00
4067256--4067305	23	2.1	24	88	3	75	0	34	4	62	1.14
4067245--4067310	28	2.4	27	78	12	71	0	30	4	65	1.13
4067349--4067430	8	10.5	8	69	23	59	58	3	0	37	1.16
4067343--4067426	5	16.6	5	73	23	61	58	3	0	38	1.16
4067345--4067427	24	3.4	24	78	11	80	59	3	0	37	1.15
4072763--4073009	50	4.8	50	81	6	248	27	21	28	21	1.99
4076997--4077232	99	2.3	103	79	7	259	21	27	22	27	1.99
4076998--4077243	49	4.8	50	82	5	255	21	27	23	28	1.99
4080734--4080774	20	2.0	20	95	0	73	46	4	17	31	1.69
4085527--4085577	2	25.5	2	100	0	102	49	0	0	50	1.00
4088045--4088089	24	1.9	23	86	4	63	31	8	2	57	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4088542--4088623	29	2.8	29	75	19	80	23	4	6	65	1.34
4088607--4088645	18	2.2	17	90	4	60	12	5	7	74	1.20
4089019--4089270	109	2.3	111	90	2	384	30	16	19	33	1.94
4092178--4092252	19	4.0	19	70	15	66	36	25	1	37	1.65
4093163--4093195	13	2.4	14	85	10	50	0	33	0	66	0.92
4101754--4101788	18	1.9	18	88	0	52	68	0	0	31	0.90
4111107--4111159	22	2.4	21	90	6	79	35	0	0	64	0.94
4111117--4111153	18	2.2	18	90	9	60	37	0	0	62	0.96
4111117--4111161	16	2.8	17	84	15	60	37	0	0	62	0.96
4111631--4111669	20	2.0	20	84	0	51	48	0	0	51	1.00
4114044--4114074	12	2.6	12	89	0	53	64	0	29	6	1.18
4119783--4119824	16	2.6	16	96	0	75	23	7	26	42	1.80
4123442--4123482	13	3.3	13	83	6	50	36	4	0	58	1.20
4128866--4128919	21	2.6	21	87	0	72	31	5	31	31	1.81
4134505--4134559	21	2.6	22	88	8	87	23	7	36	32	1.82
4145863--4145909	24	1.9	25	86	4	69	31	4	8	55	1.49
4152856--4152897	4	10.8	4	87	5	59	23	4	0	71	1.05
4152761--4152890	69	1.9	69	82	3	163	27	8	3	60	1.44
4156670--4156747	25	3.2	25	63	23	65	41	7	5	46	1.55
4156679--4156756	24	3.2	24	63	22	63	41	10	3	44	1.56
4156671--4156768	49	2.0	49	100	0	196	38	10	4	46	1.57
4158535--4158675	59	2.3	61	87	8	198	31	7	0	60	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4158666--4158824	69	2.3	69	80	2	176	26	9	4	59	1.47
4158804--4158850	4	11.8	4	86	0	58	21	6	2	70	1.20
4164474--4164543	27	2.5	28	84	11	81	38	18	1	41	1.60
4164859--4164898	20	2.0	20	90	0	62	50	12	10	27	1.72
4164847--4164913	34	1.9	35	84	3	91	46	13	8	31	1.74
4165001--4165061	23	2.5	22	82	15	68	47	11	1	39	1.50
4169099--4169182	41	2.0	42	82	11	102	50	5	4	39	1.48
4169297--4169365	31	2.2	31	80	19	81	52	2	0	44	1.16
4169636--4169686	2	25.5	2	100	0	102	49	0	0	50	1.00
4172948--4172982	18	1.9	18	94	0	61	34	28	25	11	1.91
4174425--4174585	20	8.1	20	73	15	88	59	3	1	36	1.24
4174445--4174579	9	14.9	9	73	11	98	58	0	2	38	1.16
4174505--4174558	10	5.7	10	87	10	78	70	0	1	27	0.98
4174445--4174585	10	14.3	10	71	19	75	58	1	2	37	1.19
4175075--4175107	15	2.1	17	88	11	52	24	0	6	69	1.10
4181757--4181816	31	1.9	32	89	3	95	43	11	10	35	1.75
4182650--4182725	31	2.5	31	95	0	134	42	11	17	28	1.84
4183631--4183703	36	2.0	36	86	5	103	27	13	31	27	1.94
4185534--4185597	31	2.1	31	82	11	78	37	0	0	62	0.95
4198990--4199027	11	3.5	11	100	0	76	47	26	0	26	1.52
4202113--4202321	92	2.3	91	85	5	269	45	3	4	46	1.41
4202249--4202296	26	1.9	25	84	16	64	45	0	2	52	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4202375--4202585	66	3.4	64	69	21	194	41	3	6	48	1.46
4202337--4202629	120	2.4	120	92	3	484	43	3	4	49	1.39
4202473--4202513	15	2.8	15	82	10	50	43	0	2	53	1.13
4202591--4202632	15	2.7	16	82	14	52	45	0	2	52	1.13
4202582--4202623	15	2.9	15	82	10	52	47	0	0	52	1.00
4202566--4202852	153	1.9	153	94	0	502	47	3	4	44	1.40
4206451--4206477	2	13.5	2	100	0	54	0	0	48	51	1.00
4207696--4207720	2	12.5	2	100	0	50	48	0	0	52	1.00
4208037--4208070	2	17.0	2	100	0	68	50	0	0	50	1.00
4208475--4208525	20	2.6	19	79	11	59	33	0	9	56	1.32
4222549--4222589	21	1.9	21	85	5	55	31	2	0	65	1.05
4227517--4227792	72	3.8	72	90	1	394	30	17	17	34	1.94
4230665--4231071	110	3.7	110	92	1	640	33	19	15	30	1.93
4237499--4237548	22	2.3	23	79	6	59	40	22	6	32	1.78
4245286--4245329	23	1.9	23	86	9	54	54	4	2	38	1.33
4247263--4247307	7	6.4	7	89	0	63	42	35	2	20	1.64
4248231--4248272	21	2.1	19	86	8	57	52	7	2	38	1.42
4250614--4250661	2	24.0	2	95	0	87	47	0	0	52	1.00
4251593--4251942	154	2.3	152	85	4	483	28	10	8	51	1.67
4256631--4256666	17	2.1	18	89	5	56	52	2	27	16	1.57
4259539--4259609	35	2.0	35	91	0	115	33	8	9	47	1.67
4261040--4261102	30	2.0	32	81	6	76	69	4	4	20	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4264034--4264370	160	2.1	159	94	0	593	23	16	15	45	1.85
4272735--4272814	42	2.0	41	92	5	135	41	11	15	32	1.82
4272735--4272823	42	2.2	40	88	7	128	41	10	15	32	1.81
4273067--4273114	20	2.5	20	82	3	53	20	2	33	43	1.64
4274747--4274778	2	16.0	2	100	0	64	50	0	0	50	1.00
4277246--4277270	2	12.5	2	100	0	50	52	0	0	48	1.00
4287848--4287898	25	2.0	25	88	0	75	25	39	9	25	1.86
4291030--4291065	7	5.1	7	100	0	72	13	0	30	55	1.39
4294726--4294781	26	2.2	26	83	6	69	55	7	10	26	1.60
4295089--4295149	29	2.1	29	81	0	68	36	19	19	24	1.95

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   199   200   201   202   203   204   205   206   207   208