genome.fa.s7.2.7.7.80.10.50.1000.12.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: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  60982465

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   

This is table  12  of  204  ( 24458 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)
4651466--4651541	15	5.0	15	73	16	50	34	3	5	56	1.40
4654667--4654726	22	2.7	22	92	0	93	23	26	15	35	1.94
4659312--4659351	17	2.4	17	84	16	57	75	0	0	25	0.81
4659312--4659351	9	4.9	8	85	14	55	75	0	0	25	0.81
4662243--4662314	35	2.1	35	100	0	144	30	11	18	40	1.85
4667300--4667344	2	22.5	2	100	0	90	48	0	0	51	1.00
4667597--4667652	27	2.1	27	100	0	112	39	16	0	44	1.47
4668463--4668608	43	3.4	43	93	0	240	34	26	19	19	1.96
4675148--4675190	2	21.5	2	100	0	86	51	0	48	0	1.00
4695518--4695546	14	2.1	14	100	0	58	6	13	34	44	1.71
4695883--4695937	27	2.0	27	96	0	101	41	16	14	27	1.87
4697201--4697279	35	2.3	35	88	4	115	21	17	10	50	1.75
4701634--4701798	82	2.0	82	100	0	330	31	19	14	34	1.92
4713407--4714117	355	2.0	356	99	0	1415	36	18	14	30	1.91
4714399--4715084	230	3.0	230	99	0	1363	32	15	17	34	1.91
4717385--4717428	2	23.0	2	86	9	65	50	0	0	50	1.00
4717622--4717664	20	2.2	20	87	8	61	32	0	2	65	1.06
4721857--4722056	95	2.1	95	94	2	350	41	9	5	44	1.58
4728938--4729070	63	2.1	64	92	4	225	30	4	8	56	1.49
4731717--4731788	30	2.4	30	79	9	83	33	12	8	45	1.72
4739303--4739663	185	2.0	185	88	0	542	28	19	12	39	1.89
4760378--4760410	16	2.1	16	100	0	66	51	36	6	6	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4765002--4765046	20	2.3	19	82	14	56	55	0	2	42	1.12
4765017--4765113	51	1.9	51	81	12	119	54	3	5	37	1.38
4765402--4765428	11	2.5	11	100	0	54	14	0	7	77	0.97
4787979--4788011	17	2.0	17	88	5	50	39	0	3	57	1.14
4792842--4792866	6	4.2	6	100	0	50	64	20	0	16	1.30
4792930--4792956	14	1.9	14	100	0	54	62	0	29	7	1.22
4799387--4799416	13	2.3	13	100	0	60	20	6	13	60	1.55
4800748--4800815	16	4.2	16	96	0	127	38	35	0	26	1.57
4801558--4801605	25	1.9	25	95	0	87	35	14	6	43	1.71
4819242--4819273	3	10.7	3	93	0	55	34	31	3	31	1.73
4819272--4819300	2	14.5	2	100	0	58	51	0	0	48	1.00
4836134--4836173	3	13.3	3	83	0	53	5	2	65	27	1.27
4836276--4836306	3	10.3	3	92	0	53	35	0	32	32	1.58
4839871--4839904	17	2.0	17	100	0	68	41	0	0	58	0.98
4840139--4840174	16	2.2	16	100	0	72	38	36	0	25	1.56
4840687--4840754	16	4.2	16	96	0	127	38	5	33	22	1.78
4840734--4840824	46	2.0	46	91	4	150	27	4	29	38	1.76
4840983--4841021	17	2.5	15	84	15	60	61	0	0	38	0.96
4840988--4841021	17	2.0	17	100	0	68	58	0	0	41	0.98
4841054--4841093	20	2.0	21	85	5	55	60	5	0	35	1.19
4841061--4841120	26	2.2	27	82	14	79	56	3	0	40	1.16
4841183--4841246	32	2.0	32	81	0	74	50	1	0	48	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4842509--4842612	49	2.1	49	87	0	145	50	9	8	30	1.65
4844958--4845015	29	2.0	29	100	0	116	27	10	10	51	1.68
4845444--4845504	25	2.4	25	97	0	113	45	19	4	29	1.71
4847508--4847533	13	2.0	13	100	0	52	30	15	38	15	1.88
4847657--4847750	45	2.1	46	91	2	154	20	10	52	17	1.73
4861511--4861572	31	2.2	30	83	13	78	38	1	3	56	1.25
4875183--4875232	20	2.6	19	84	6	66	50	4	4	42	1.40
4879254--4879409	46	3.5	46	92	2	255	33	16	22	27	1.95
4880281--4880334	16	3.4	16	87	5	74	37	24	0	38	1.56
4882612--4882700	27	3.5	26	77	13	96	49	0	4	46	1.22
4882613--4882692	25	3.2	24	73	16	74	48	0	5	46	1.24
4887318--4887374	12	5.1	12	72	21	52	38	19	5	36	1.74
4887310--4887374	33	2.0	33	96	0	121	38	20	6	35	1.77
4896612--4896642	2	15.5	2	100	0	62	51	0	0	48	1.00
4897986--4898040	20	2.8	20	77	2	58	81	1	12	3	0.89
4898601--4898632	14	2.4	14	90	10	50	3	25	0	71	1.00
4915110--4915144	6	5.8	6	100	0	70	17	48	17	17	1.81
4923977--4924047	31	2.1	34	82	10	85	32	14	30	22	1.93
4924255--4924282	9	3.1	9	100	0	56	57	10	0	32	1.33
4924225--4924434	68	3.1	68	95	1	379	45	8	4	40	1.56
4924323--4924350	9	3.1	9	100	0	56	57	10	0	32	1.33
4932194--4932233	3	13.3	3	100	0	80	0	32	0	67	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4934524--4934559	7	5.1	7	90	10	56	58	2	0	38	1.13
4938553--4938726	85	2.0	85	92	0	285	37	14	20	27	1.92
4941382--4941569	67	3.0	61	83	12	238	35	7	17	39	1.79
4941471--4941508	20	1.9	20	88	0	58	18	5	28	47	1.70
4963304--4963452	76	2.0	76	100	0	298	29	11	17	41	1.84
4966448--4966494	15	3.2	14	80	11	58	31	2	0	65	1.04
4967289--4967318	2	15.0	2	100	0	60	50	0	0	50	1.00
4982407--4982443	19	1.9	19	89	10	58	16	5	32	45	1.70
4982410--4982455	18	2.5	19	82	3	58	10	6	36	45	1.65
4983981--4984020	20	2.0	21	85	5	55	2	12	7	77	1.07
4996414--4996478	29	2.2	29	78	5	69	47	7	1	43	1.41
4997455--4997557	49	2.1	49	100	0	206	36	5	21	35	1.78
5000591--5000680	9	9.6	9	80	9	99	38	25	8	26	1.85
5000589--5000680	20	4.8	20	82	7	111	40	25	8	26	1.84
5000591--5000680	29	3.2	28	82	14	105	38	25	8	26	1.85
5000678--5000789	37	3.0	37	90	0	179	46	15	4	33	1.66
5000678--5000730	20	2.9	18	75	8	54	49	16	1	32	1.57
5000687--5000784	17	5.4	17	65	13	52	48	14	4	32	1.62
5001116--5001171	26	2.2	26	83	6	69	30	3	10	55	1.51
5002081--5002120	16	2.5	16	91	0	62	25	2	35	37	1.69
5004075--5004107	12	2.8	12	90	4	50	42	33	18	6	1.75
5013355--5013379	2	12.5	2	100	0	50	52	0	48	0	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5019893--5019921	2	14.5	2	100	0	58	51	0	0	48	1.00
5022490--5022529	20	2.0	20	90	0	62	32	22	5	40	1.76
5024554--5024579	11	2.4	11	100	0	52	53	0	7	38	1.30
5024576--5024635	9	6.4	9	75	21	61	71	0	1	26	0.95
5024565--5024673	28	4.1	27	69	19	79	64	0	4	31	1.14
5024526--5024673	40	3.7	40	84	10	196	62	0	4	33	1.14
5024602--5024633	16	2.0	16	93	0	55	71	0	0	28	0.86
5024585--5024647	29	2.1	29	80	13	67	66	0	3	30	1.07
5024633--5024657	11	2.3	11	100	0	50	52	0	8	40	1.31
5026707--5026741	4	8.8	4	100	0	70	51	22	0	25	1.48
5036691--5036774	21	4.0	21	87	4	116	38	25	21	15	1.92
5036691--5036774	44	2.0	41	86	6	114	38	25	21	15	1.92
5037805--5037851	3	15.7	3	84	8	51	57	2	0	40	1.11
5037805--5037852	8	5.8	8	82	2	51	56	2	0	41	1.11
5037810--5037858	24	2.0	25	88	4	73	51	2	0	46	1.12
5037805--5037853	19	2.7	20	75	15	52	55	2	0	42	1.11
5040963--5041049	12	7.2	12	66	14	54	12	35	24	27	1.92
5040879--5041078	24	8.2	24	86	4	222	17	31	25	26	1.97
5050473--5050602	13	10.0	13	68	12	70	34	19	3	43	1.67
5050558--5050629	26	2.7	26	74	6	65	31	20	5	41	1.76
5052323--5052382	21	3.0	21	87	4	88	15	25	18	41	1.89
5053781--5053878	49	2.0	49	100	0	196	24	20	18	36	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5053945--5053990	17	2.6	18	82	6	58	43	21	4	30	1.72
5058756--5059011	51	5.1	51	85	4	272	16	32	25	26	1.96
5058756--5058989	24	9.4	24	84	6	243	16	32	25	26	1.96
5058891--5058982	12	7.7	12	65	13	55	15	32	22	29	1.95
5062093--5062129	14	2.5	14	91	8	56	81	0	16	2	0.81
5071873--5071919	16	2.9	16	78	6	51	31	4	4	59	1.36
5072174--5072297	57	2.2	57	98	0	239	32	18	18	30	1.95
5088884--5089021	29	4.9	29	77	12	169	33	5	23	37	1.79
5089741--5089814	19	3.8	19	92	1	112	35	8	16	40	1.78
5089988--5090026	19	2.0	21	85	10	55	15	10	5	69	1.34

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