genome.fa.s11.2.7.7.80.10.50.1000.10.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: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62681010

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   
          209   210   

This is table  10  of  210  ( 25152 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)
3837043--3837088	14	3.3	14	84	0	65	54	4	2	39	1.32
3837031--3837075	21	2.1	22	83	4	56	55	4	0	40	1.20
3837043--3837095	28	1.9	27	92	3	88	52	5	1	39	1.36
3844359--3844880	165	3.2	164	91	1	810	21	22	24	30	1.99
3851819--3851856	18	2.1	19	90	5	60	44	0	31	23	1.54
3852693--3852738	24	1.9	24	86	8	67	47	0	4	47	1.21
3853741--3853803	31	2.0	31	82	11	76	39	4	0	55	1.21
3853800--3853843	18	2.5	17	82	13	54	40	0	6	52	1.28
3853803--3853857	20	2.9	18	81	15	58	38	0	5	56	1.23
3866245--3866278	2	17.0	2	100	0	68	50	0	0	50	1.00
3868057--3868083	7	3.9	7	100	0	54	85	0	0	14	0.61
3872381--3872451	27	2.6	28	77	6	92	19	30	36	12	1.89
3872493--3872611	38	3.5	33	75	19	102	65	0	31	2	1.06
3872515--3872603	10	9.8	9	75	19	62	68	0	28	3	1.05
3872518--3872600	24	3.4	23	82	15	89	68	0	27	3	1.06
3872515--3872603	5	19.8	4	75	22	56	68	0	28	3	1.05
3872506--3872605	10	10.3	10	75	15	59	66	0	31	3	1.07
3872522--3872648	54	2.4	54	80	9	145	67	1	28	2	1.12
3872586--3872649	34	1.9	33	83	3	83	65	3	31	0	1.08
3873031--3873082	13	4.0	13	75	9	52	65	7	1	25	1.30
3872957--3873314	156	2.3	154	86	7	510	49	8	11	30	1.69
3875769--3875896	39	3.3	38	78	8	141	48	10	5	35	1.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3875786--3875881	40	2.4	39	84	5	113	47	11	4	36	1.59
3876245--3876293	23	2.1	23	82	17	57	28	0	4	67	1.09
3885904--3885934	16	1.9	16	93	0	53	48	3	0	48	1.17
3888286--3888332	2	23.5	2	100	0	94	51	0	0	48	1.00
3894930--3894963	10	3.1	11	87	12	52	29	0	0	70	0.87
3906896--3906932	19	2.0	18	89	5	56	75	0	2	21	0.92
3908296--3908339	21	2.0	21	82	4	52	56	0	36	6	1.26
3910154--3910203	22	2.3	22	79	6	57	58	6	10	26	1.54
3914437--3914467	8	3.9	8	95	0	53	67	0	0	32	0.91
3917815--3917886	19	3.8	18	70	17	56	62	1	2	33	1.18
3917807--3917922	58	2.0	59	86	6	164	62	1	6	30	1.29
3917826--3917926	39	2.6	39	77	10	102	64	1	5	27	1.28
3917795--3917906	29	3.9	28	78	15	113	59	3	5	31	1.37
3917807--3917949	10	14.9	10	67	17	63	61	2	5	30	1.30
3918165--3918245	30	2.8	28	81	7	90	29	4	0	65	1.13
3918165--3918269	28	3.7	28	77	8	88	27	3	0	67	1.14
3918229--3918269	17	2.3	18	80	16	50	19	0	2	78	0.87
3918374--3918635	90	2.9	89	80	8	267	38	9	14	37	1.80
3918374--3918606	94	2.5	94	82	6	255	38	10	14	36	1.80
3933553--3933594	18	2.6	16	81	11	50	28	2	19	50	1.60
3941386--3941447	19	3.3	18	75	18	56	29	0	3	67	1.06
3943083--3943132	23	2.1	24	85	7	66	28	0	6	66	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3945748--3945777	14	2.1	14	93	0	51	53	16	0	30	1.44
3948219--3948492	138	2.0	138	90	1	433	33	19	17	28	1.95
3948249--3948522	138	2.0	137	80	6	306	37	18	19	24	1.94
3961243--3961280	17	2.2	17	100	0	76	42	10	18	28	1.83
3970648--3970691	21	2.1	21	100	0	88	18	4	18	59	1.55
3970708--3970750	21	2.0	21	82	8	52	37	0	6	55	1.27
3970767--3970812	18	2.6	18	86	3	58	43	0	2	54	1.12
3970743--3970848	55	1.9	54	81	7	124	44	0	5	49	1.32
3970966--3971057	44	2.1	44	82	11	109	35	25	6	32	1.81
3971040--3971078	16	2.5	16	95	4	71	28	30	7	33	1.85
3971217--3971284	23	2.9	23	80	2	82	27	8	17	45	1.78
3971221--3971300	23	3.4	23	81	5	81	31	7	17	43	1.77
3979038--3979190	4	38.2	4	98	0	297	49	24	0	25	1.55
3985351--3985501	75	2.0	76	97	1	286	45	6	22	25	1.77
3993691--3993751	28	2.2	28	94	5	106	27	8	21	42	1.81
4003943--4004077	55	2.5	51	79	12	146	29	16	11	42	1.82
4003965--4004085	55	2.2	56	89	1	190	28	15	9	46	1.78
4007049--4007075	11	2.5	11	100	0	54	0	0	81	18	0.69
4007609--4007633	13	1.9	13	100	0	50	24	4	0	72	1.02
4020077--4020119	6	7.0	6	86	5	50	16	6	0	76	0.99
4020077--4020119	12	3.5	12	90	3	59	16	6	0	76	0.99
4020079--4020119	18	2.2	19	91	4	66	17	7	0	75	1.02
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4021054--4021098	23	2.0	22	87	12	65	33	4	0	62	1.15
4021565--4021590	7	3.7	7	100	0	52	38	0	0	61	0.96
4021566--4021610	14	3.1	14	87	6	54	33	6	0	60	1.23
4021954--4022009	21	2.7	21	85	0	76	30	8	32	28	1.88
4022590--4022817	113	2.0	113	98	0	438	35	18	14	31	1.91
4026626--4026655	2	15.5	2	93	6	53	53	0	0	46	1.00
4027375--4027407	17	1.9	17	93	0	57	42	6	24	27	1.78
4030875--4030907	17	1.9	17	93	0	57	45	6	24	24	1.75
4032158--4032208	26	2.0	26	88	3	77	62	1	0	35	1.06
4032161--4032253	33	2.8	33	66	18	77	61	1	1	36	1.10
4032764--4032807	22	2.0	23	90	4	72	34	0	0	65	0.93
4033114--4033185	35	2.1	35	97	0	135	51	5	11	31	1.60
4034589--4034639	2	25.5	2	100	0	102	49	0	0	50	1.00
4036812--4036857	24	2.0	23	83	12	58	8	2	32	56	1.42
4037743--4037863	42	2.8	43	82	6	147	23	16	27	32	1.96
4037751--4037863	43	2.7	42	81	12	124	24	16	27	30	1.97
4039696--4039736	2	20.5	2	94	0	73	51	2	0	46	1.14
4044860--4044901	22	2.0	22	90	4	68	59	2	4	33	1.31
4044909--4044959	22	2.5	19	73	20	50	37	7	1	52	1.42
4050865--4050970	54	2.0	54	90	3	169	16	13	50	18	1.77
4054774--4054808	4	8.8	4	100	0	70	74	0	25	0	0.82
4063424--4063453	12	2.5	12	94	0	51	53	0	23	23	1.46
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4065810--4065857	23	2.0	24	88	4	71	22	4	6	66	1.32
4068330--4068392	30	2.1	30	87	0	90	58	12	1	26	1.43
4071398--4071422	13	1.9	13	100	0	50	36	24	8	32	1.84
4073074--4073142	34	2.0	34	97	0	129	53	2	36	7	1.44
4079135--4079182	17	2.8	17	87	6	62	47	2	2	47	1.25
4079365--4079497	40	3.2	40	75	14	149	48	3	9	39	1.50
4079338--4079497	87	1.8	87	98	0	311	46	3	10	40	1.53
4079338--4079477	47	3.1	47	76	14	186	45	3	10	40	1.56
4080117--4080215	31	3.2	31	74	7	85	37	14	10	38	1.79
4091671--4091863	9	20.6	9	70	16	108	61	1	3	34	1.18
4091789--4091862	28	2.6	28	80	15	89	63	1	4	31	1.21
4091747--4091863	48	2.4	47	77	14	114	62	0	2	34	1.15
4091802--4091865	20	3.2	20	71	8	58	67	1	3	28	1.15
4092296--4092410	16	6.3	19	65	26	54	34	2	0	62	1.09
4092304--4092438	9	14.9	9	68	19	59	33	2	1	62	1.19
4092362--4092425	17	3.7	16	75	17	65	31	4	1	62	1.25
4095657--4095823	10	16.8	10	70	15	89	64	2	2	31	1.19
4095657--4095719	19	3.4	18	78	8	65	68	1	1	28	1.08
4095655--4095821	9	17.1	9	68	20	63	64	2	2	31	1.19
4096170--4096247	28	2.7	28	80	9	95	30	0	3	65	1.10
4096170--4096243	10	7.7	10	71	14	57	31	0	4	64	1.12
4096169--4096327	19	8.9	17	73	15	85	32	1	2	63	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4096147--4096325	9	19.8	9	68	20	56	32	1	2	62	1.19
4104799--4104846	25	1.9	25	86	0	69	35	6	2	56	1.36
4104794--4104851	25	2.4	24	77	8	64	39	5	1	53	1.33
4105880--4105922	19	2.2	19	83	8	50	16	13	16	53	1.73
4109247--4109285	19	2.1	18	90	4	60	35	2	5	56	1.35
4109213--4109316	9	11.3	10	66	21	50	34	4	1	58	1.30
4121262--4121380	62	2.0	60	89	3	184	41	5	10	43	1.60
4130168--4130534	46	7.6	47	87	7	397	34	14	22	28	1.93
4130168--4130534	98	3.7	97	85	9	501	34	14	22	28	1.93
4130182--4130534	196	1.8	196	92	0	607	35	14	22	28	1.93

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   
          209   210