genome.fa.s5.2.7.7.80.10.50.1000.16.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  16  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)
4860843--4860879	17	2.2	17	90	0	56	56	18	24	0	1.41
4860874--4860920	19	2.5	19	86	6	60	25	40	23	10	1.87
4861501--4861616	17	6.4	18	79	14	89	34	13	9	42	1.77
4861507--4861629	35	3.5	36	83	6	171	30	16	10	42	1.82
4862059--4862084	12	2.2	12	100	0	52	61	7	7	23	1.49
4865521--4865621	27	3.7	26	74	16	87	15	7	33	42	1.76
4865542--4865726	57	3.4	57	67	20	178	15	10	32	41	1.81
4865509--4865772	105	2.5	105	86	4	304	14	10	33	41	1.80
4865701--4866003	45	6.7	45	82	5	326	13	16	29	41	1.86
4865557--4865774	105	2.1	104	94	2	386	13	11	32	41	1.81
4865701--4865979	90	3.1	89	88	3	389	12	16	29	42	1.84
4865731--4865992	135	1.9	135	89	3	411	12	17	28	41	1.86
4867121--4867264	74	1.9	74	88	2	218	33	17	19	29	1.95
4867612--4867708	51	1.9	51	89	8	153	54	0	8	37	1.30
4874554--4875045	45	10.7	45	73	13	331	12	15	29	43	1.83
4874656--4875045	90	4.3	90	88	0	539	11	15	29	43	1.82
4874656--4875052	45	8.8	44	78	6	375	11	15	28	43	1.82
4875391--4875431	20	2.0	20	100	0	82	36	24	19	19	1.95
4876141--4876268	64	2.0	64	96	0	238	26	11	15	46	1.80
4877565--4877603	19	2.1	18	85	4	51	38	7	10	43	1.67
4884353--4884403	21	2.4	21	80	6	59	50	3	0	45	1.20
4885922--4885955	17	2.0	17	94	0	59	38	17	11	32	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4886532--4886923	90	4.4	90	92	3	528	11	18	29	40	1.86
4886541--4886923	180	2.1	177	93	1	658	11	18	28	41	1.85
4886541--4886923	45	8.6	45	81	6	447	11	18	28	41	1.85
4888249--4888279	16	2.0	15	93	6	53	0	9	0	90	0.46
4888244--4888279	11	3.3	11	92	0	54	0	13	0	86	0.58
4888494--4888524	15	2.1	14	94	5	53	0	9	0	90	0.46
4888088--4889062	245	4.0	245	97	2	1809	28	16	7	48	1.73
4888493--4888522	10	3.0	10	95	0	51	0	13	0	86	0.57
4888739--4888770	15	2.2	14	94	5	55	0	9	0	90	0.45
4889398--4889434	17	2.2	17	90	0	56	27	24	5	43	1.76
4889974--4890016	9	4.8	9	97	0	68	44	16	11	27	1.82
4891886--4891948	26	2.5	26	82	12	78	61	4	4	28	1.36
4892101--4892143	12	3.6	12	78	12	52	69	0	2	27	1.00
4893744--4893790	22	2.1	22	84	0	58	46	17	17	19	1.84
4893782--4893916	32	4.3	32	79	5	132	40	22	16	21	1.91
4893963--4894026	27	2.4	27	82	12	71	31	21	25	21	1.98
4894091--4894196	24	4.4	24	81	0	104	44	25	6	23	1.77
4894103--4894199	48	2.0	47	86	7	133	44	24	6	24	1.77
4894105--4894201	24	4.0	24	80	6	108	43	25	6	24	1.77
4894193--4894278	26	3.3	26	78	3	73	25	18	20	34	1.96
4894222--4894401	27	6.7	27	81	7	118	18	17	23	41	1.90
4894243--4894411	27	6.3	27	82	6	200	18	15	23	42	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4894260--4894411	80	1.9	81	86	1	216	17	15	24	42	1.88
4895344--4895400	13	4.7	13	79	16	77	40	45	0	14	1.44
4895354--4895399	22	2.0	23	91	4	76	41	47	0	10	1.38
4895332--4895399	18	3.8	18	74	3	66	41	42	0	16	1.48
4895385--4895497	39	2.9	39	93	1	183	52	24	2	20	1.59
4895632--4895694	17	3.5	17	69	12	54	34	3	12	49	1.57
4895629--4895703	37	2.0	37	94	0	114	36	4	14	45	1.64
4895702--4895732	9	3.4	9	95	0	53	25	9	22	41	1.84
4898577--4898608	15	2.1	15	94	0	55	15	6	9	68	1.36
4899447--4899494	25	1.9	25	83	8	62	41	10	8	39	1.69
4902991--4903056	29	2.2	29	84	7	80	40	1	0	57	1.08
4904733--4904821	45	2.0	46	84	6	119	23	6	1	68	1.20
4904748--4904866	4	29.5	4	68	14	66	23	8	0	67	1.23
4904961--4904990	14	2.1	15	93	6	53	26	6	0	66	1.16
4905224--4905292	26	2.7	25	78	8	68	40	4	2	52	1.36
4916655--4916820	44	3.6	44	79	11	174	31	19	19	29	1.97
4917957--4918016	21	2.8	22	75	14	79	20	30	25	25	1.99
4918578--4918630	10	5.2	10	78	17	56	66	3	30	0	1.10
4922084--4922275	102	1.9	101	84	5	255	14	15	31	39	1.87
4922192--4922499	90	3.4	90	84	3	388	13	16	26	42	1.86
4922192--4922492	135	2.2	135	81	5	349	13	16	27	42	1.86
4922192--4922498	45	6.8	45	81	5	309	13	16	27	42	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4925109--4925146	19	2.0	19	90	10	60	65	0	2	31	1.06
4926450--4926508	27	2.1	29	87	6	86	67	13	3	15	1.35
4932215--4932250	19	1.9	18	88	5	54	55	22	0	22	1.44
4955542--4955601	30	2.0	30	96	0	111	56	11	3	28	1.51
4955636--4955665	14	2.1	14	93	0	51	63	13	6	16	1.50
4962524--4962554	2	15.5	2	100	0	62	51	0	0	48	1.00
4962970--4963006	2	18.5	2	88	0	56	48	0	2	48	1.15
4962978--4963012	10	3.5	10	92	0	52	45	0	5	48	1.26
4963791--4963925	70	1.9	70	100	0	270	43	13	7	35	1.72
4967134--4967187	22	2.5	22	88	11	85	22	29	1	46	1.62
4967134--4967187	11	5.1	11	85	10	69	22	29	1	46	1.62
4969032--4969074	18	2.4	18	88	0	59	18	27	9	44	1.80
4969315--4969362	21	2.3	21	82	7	62	35	39	18	6	1.76
4969315--4969370	21	2.7	21	80	5	60	33	42	16	7	1.75
4981503--4981537	18	2.0	17	88	5	52	2	17	2	77	1.02
4984267--4984296	15	2.0	15	93	0	51	56	0	0	43	0.99
4995368--4995406	2	19.5	2	100	0	78	48	0	0	51	1.00
5000097--5000205	55	2.0	55	96	0	200	50	19	12	17	1.78
5019532--5019599	23	3.2	23	62	33	60	42	2	7	47	1.46
5019519--5019603	41	2.1	41	97	0	161	45	2	5	45	1.40
5023225--5023267	16	3.0	14	83	10	52	58	0	0	41	0.98
5023228--5023267	13	2.8	13	85	14	53	60	0	0	40	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5027957--5027995	21	1.9	20	84	5	51	15	10	23	51	1.73
5029302--5029332	10	3.1	10	90	0	53	77	0	3	19	0.90
5039565--5039596	15	2.3	15	89	10	50	62	21	0	15	1.32
5044735--5044772	15	2.5	15	91	0	58	28	10	34	26	1.90
5049323--5049456	40	3.4	39	76	11	148	31	24	17	26	1.97
5049323--5049456	37	3.4	41	75	9	152	31	24	17	26	1.97
5050339--5050401	5	12.8	5	75	18	53	0	19	6	74	1.02
5051029--5051090	30	2.1	30	96	0	115	48	9	6	35	1.62
5052392--5052451	25	2.4	25	85	0	84	16	13	15	55	1.70
5057416--5057477	26	2.5	24	76	7	61	32	19	20	27	1.97
5067000--5067072	27	2.8	26	76	15	62	41	1	1	56	1.16
5067002--5067072	26	2.8	25	74	16	65	42	1	1	54	1.17
5067237--5067287	16	3.3	15	75	20	52	54	1	1	41	1.22
5075468--5075666	34	5.8	34	82	2	209	40	17	21	20	1.91
5075468--5075667	69	2.9	68	82	2	211	41	17	21	20	1.91
5075478--5075666	103	1.8	103	94	0	333	40	17	21	20	1.91
5075904--5075941	14	2.8	13	88	7	58	34	10	7	47	1.67
5081630--5081671	22	1.9	22	95	0	75	61	11	0	26	1.30
5081631--5081677	11	4.4	11	81	2	60	61	10	0	27	1.29
5083367--5083421	24	2.3	23	87	12	76	36	1	3	58	1.26
5083367--5083436	24	2.9	24	81	10	63	37	1	2	58	1.22
5088871--5088926	14	3.8	14	84	11	76	39	21	5	33	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5088871--5088919	17	3.1	17	69	25	52	40	22	4	32	1.73
5093201--5093370	58	3.0	58	81	7	186	22	14	17	45	1.85
5097378--5097494	51	2.3	51	94	2	200	35	13	23	28	1.93
5100881--5100924	21	2.1	21	82	0	52	36	4	0	59	1.18
5100880--5100948	28	2.4	28	85	9	86	40	4	1	53	1.30
5101050--5101091	20	2.1	20	100	0	84	33	4	19	42	1.72
5103299--5103334	17	2.2	17	90	5	56	50	36	5	8	1.56
5104272--5104330	3	19.7	3	100	0	118	32	0	0	67	0.91
5106828--5106870	18	2.3	18	84	4	50	39	2	2	55	1.25
5108259--5108312	28	1.9	28	85	7	74	62	3	7	25	1.38

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